You can subscribe to this list here.
2010 |
Jan
|
Feb
|
Mar
|
Apr
(1) |
May
(4) |
Jun
(2) |
Jul
(3) |
Aug
(3) |
Sep
(5) |
Oct
(2) |
Nov
(4) |
Dec
|
---|---|---|---|---|---|---|---|---|---|---|---|---|
2011 |
Jan
(12) |
Feb
|
Mar
(5) |
Apr
(6) |
May
|
Jun
|
Jul
(1) |
Aug
|
Sep
|
Oct
(15) |
Nov
(3) |
Dec
|
2012 |
Jan
|
Feb
(7) |
Mar
(3) |
Apr
(17) |
May
(5) |
Jun
|
Jul
(5) |
Aug
(1) |
Sep
(2) |
Oct
(3) |
Nov
(2) |
Dec
(1) |
2013 |
Jan
|
Feb
|
Mar
|
Apr
|
May
(4) |
Jun
|
Jul
(1) |
Aug
|
Sep
(2) |
Oct
(2) |
Nov
(2) |
Dec
(2) |
2014 |
Jan
|
Feb
(2) |
Mar
(9) |
Apr
(2) |
May
|
Jun
(2) |
Jul
(1) |
Aug
(1) |
Sep
|
Oct
|
Nov
(1) |
Dec
(1) |
2015 |
Jan
|
Feb
|
Mar
(4) |
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
2017 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
(1) |
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
From: David N. <Dav...@hc...> - 2012-02-16 17:20:10
|
Yes, USeq should work for you. Many folks are using it for RIP-Seq analysis. It makes a direct comparison between the number of reads in a given window between a treatment and control. The total number of reads in each dataset are used to set the expectation of success for the binomial p-value test. Thus if you have 10x the amount of data in the input then an "even" distribution of reads between treatment and control would be 1:10. If you have replicas use the MultipleReplicaScanSeqs which wraps the DESeq package to control for overdispersion in your data. -cheers, D From: mali salmon <sha...@gm...<mailto:sha...@gm...>> Date: Thu, 16 Feb 2012 01:51:20 -0700 To: David Nix <dav...@hc...<mailto:dav...@hc...>>, "use...@li...<mailto:use...@li...>" <use...@li...<mailto:use...@li...>> Subject: RNA-IP analysis with Useq Dear Useq-users Is it possible to analyse RNA-IP data using Useq? I have IP and Input data from RNA that was fragmented to 100nt, and then treated with an antibody against a specific RNA methylation. I aligned reads to the genome (I don't care of junctions reads, and only 10% of the data couldn't be mapped to the genome), and I would like to find enriched regions in IP compared to Input. The idea is similar to ChIP-seq, but I'm wondering if there are special issues I should taking care of since the reads are coming from the transcriptome and not the genome. For example, in ChIP-seq finding tools like MACS and others, I should give as parameter the effective genome size. When I run MACS (sorry I haven't tried Useq with this data yet) with gsize=transcriptome size, I get ~2000 peaks, however, when I run it with gsize=genome I get ~22000 peaks. In a genome browser, those peaks that were missed with smaller gsize look real by looking them in a genome browser and comparing them with their Input. Hence I thought of finding a tool that can compare IP directly to Input without taking into account a random expectations calculated based on the genome size. Is it make sense? Is it possible to do it with Useq? Looking forward to your reply Thanks Mali |
From: mali s. <sha...@gm...> - 2012-02-16 08:51:29
|
Dear Useq-users Is it possible to analyse RNA-IP data using Useq? I have IP and Input data from RNA that was fragmented to 100nt, and then treated with an antibody against a specific RNA methylation. I aligned reads to the genome (I don't care of junctions reads, and only 10% of the data couldn't be mapped to the genome), and I would like to find enriched regions in IP compared to Input. The idea is similar to ChIP-seq, but I'm wondering if there are special issues I should taking care of since the reads are coming from the transcriptome and not the genome. For example, in ChIP-seq finding tools like MACS and others, I should give as parameter the effective genome size. When I run MACS (sorry I haven't tried Useq with this data yet) with gsize=transcriptome size, I get ~2000 peaks, however, when I run it with gsize=genome I get ~22000 peaks. In a genome browser, those peaks that were missed with smaller gsize look real by looking them in a genome browser and comparing them with their Input. Hence I thought of finding a tool that can compare IP directly to Input without taking into account a random expectations calculated based on the genome size. Is it make sense? Is it possible to do it with Useq? Looking forward to your reply Thanks Mali |
From: David N. <Dav...@hc...> - 2012-02-08 22:53:53
|
Hello Andrew, This is easily fixed, it is looking at /usr/bin/java . I'll just disable it. The apps will choke if run on 1.4 and throw an error message so no need to check. -cheers, D On 2/6/12 12:37 PM, "Oler, Andrew (NIH/NIAID) [C]" <and...@ni...> wrote: >Hi David, > >I'm running the ChIPSeq application from USeq 8.0.7 and I'm getting this >error: > >The following problems were encountered when processing your parameter >file. Correct and restart. -> >Your java application is not >= 1.6 (type 'java -version' on the cmd >line). Install the most recent java from http://www.java.com/en/download/ >. >Your save results directory exits, may overwrite the files within. > >When I type java -version on the command line, I get this output: >java -version >java version "1.6.0_22" >Java(TM) SE Runtime Environment (build 1.6.0_22-b04) >Java HotSpot(TM) 64-Bit Server VM (build 17.1-b03, mixed mode) > >The java version is fine, so I'm not sure what the problem is. java is >an alias for a locally installed version of java, which is 1.6. Could it >be that the ChIPSeq program calls '/usr/bin/java' instead of 'java'? > >/usr/bin/java -version >java version "1.4.2" >gij (GNU libgcj) version 4.1.2 20080704 (Red Hat 4.1.2-46) > >Copyright (C) 2006 Free Software Foundation, Inc. >This is free software; see the source for copying conditions. There is NO >warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR >PURPOSE. > >I'm running this on a system where I can't change the binaries in >/usr/bin/. Any suggestions? > >Thanks, > >Andrew > >Andrew Oler, Ph.D. >Contractor - Lockheed Martin >High-Throughput Sequencing Bioinformatics Specialist >Computational Biology Section >Bioinformatics and Computational Biosciences Branch (BCBB) >OCICB/OSMO/OD/NIAID/NIH > >31 Center Drive, Room 3B62 >Bethesda, MD 20892 >Mobile: 240-507-3791 >Office: 301-402-5685 >http://bioinformatics.niaid.nih.gov<http://bioinformatics.niaid.nih.gov/> >(Within NIH) >http://exon.niaid.nih.gov<http://exon.niaid.nih.gov/> (Public) > >Disclaimer: The information in this e-mail and any of its attachments is >confidential and may contain sensitive information. It should not be used >by anyone who is not the original intended recipient. If you have >received this e-mail in error please inform the sender and delete it from >your mailbox or any other storage devices. National Institute of Allergy >and Infectious Diseases shall not accept liability for any statements >made that are sender's own and not expressly made on behalf of the NIAID >by one of its representatives. > |
From: Nicholas D. <Nic...@gl...> - 2012-02-07 08:49:43
|
Can you edit your path (depending on your shell either export PATH= in bash or set PATH for tcsh) and reset it completely so it doesn't look in /usr/bin ... temporarily resetting it while you are using Useq. Best wishes, Nick Nick Dickens DPhil BSc ARCS Genome and Data Analyst Wellcome Trust Centre for Molecular Parasitology B6-21 Glasgow Biomedical Research Centre 120 University Place Glasgow G12 8TA, UK Tel: +44 (0)141 330 8282 -----Original Message----- From: Oler, Andrew (NIH/NIAID) [C] [mailto:and...@ni...] Sent: Mon 2012-02-06 19:37 To: David Nix Cc: use...@li... Subject: [Useq-users] ChIPSeq java error Hi David, I'm running the ChIPSeq application from USeq 8.0.7 and I'm getting this error: The following problems were encountered when processing your parameter file. Correct and restart. -> Your java application is not >= 1.6 (type 'java -version' on the cmd line). Install the most recent java from http://www.java.com/en/download/ . Your save results directory exits, may overwrite the files within. When I type java -version on the command line, I get this output: java -version java version "1.6.0_22" Java(TM) SE Runtime Environment (build 1.6.0_22-b04) Java HotSpot(TM) 64-Bit Server VM (build 17.1-b03, mixed mode) The java version is fine, so I'm not sure what the problem is. java is an alias for a locally installed version of java, which is 1.6. Could it be that the ChIPSeq program calls '/usr/bin/java' instead of 'java'? /usr/bin/java -version java version "1.4.2" gij (GNU libgcj) version 4.1.2 20080704 (Red Hat 4.1.2-46) Copyright (C) 2006 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. I'm running this on a system where I can't change the binaries in /usr/bin/. Any suggestions? Thanks, Andrew Andrew Oler, Ph.D. Contractor - Lockheed Martin High-Throughput Sequencing Bioinformatics Specialist Computational Biology Section Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62 Bethesda, MD 20892 Mobile: 240-507-3791 Office: 301-402-5685 http://bioinformatics.niaid.nih.gov<http://bioinformatics.niaid.nih.gov/> (Within NIH) http://exon.niaid.nih.gov<http://exon.niaid.nih.gov/> (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ------------------------------------------------------------------------------ Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 _______________________________________________ Useq-users mailing list Use...@li... https://lists.sourceforge.net/lists/listinfo/useq-users |
From: Oler, A. (NIH/N. [C] <and...@ni...> - 2012-02-06 19:37:12
|
Hi David, I'm running the ChIPSeq application from USeq 8.0.7 and I'm getting this error: The following problems were encountered when processing your parameter file. Correct and restart. -> Your java application is not >= 1.6 (type 'java -version' on the cmd line). Install the most recent java from http://www.java.com/en/download/ . Your save results directory exits, may overwrite the files within. When I type java -version on the command line, I get this output: java -version java version "1.6.0_22" Java(TM) SE Runtime Environment (build 1.6.0_22-b04) Java HotSpot(TM) 64-Bit Server VM (build 17.1-b03, mixed mode) The java version is fine, so I'm not sure what the problem is. java is an alias for a locally installed version of java, which is 1.6. Could it be that the ChIPSeq program calls '/usr/bin/java' instead of 'java'? /usr/bin/java -version java version "1.4.2" gij (GNU libgcj) version 4.1.2 20080704 (Red Hat 4.1.2-46) Copyright (C) 2006 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. I'm running this on a system where I can't change the binaries in /usr/bin/. Any suggestions? Thanks, Andrew Andrew Oler, Ph.D. Contractor - Lockheed Martin High-Throughput Sequencing Bioinformatics Specialist Computational Biology Section Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62 Bethesda, MD 20892 Mobile: 240-507-3791 Office: 301-402-5685 http://bioinformatics.niaid.nih.gov<http://bioinformatics.niaid.nih.gov/> (Within NIH) http://exon.niaid.nih.gov<http://exon.niaid.nih.gov/> (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. |
From: Don D. <don...@hs...> - 2012-02-02 17:35:28
|
I registered for sourceforge on Tuesday but still am unable to report bugs. I am logged out everytime. Any suggestions? Thanks, Don A. Delker, Ph.D. Research Assistant Professor School of Medicine University of Utah, SOM 4R118 30 North 1900 East Salt Lake City, UT 84132 |
From: David N. <Dav...@hc...> - 2011-11-04 20:46:19
|
Hello Folks, I added an option to the SamTranscriptomeParser to reverse the strand of the 2nd read for paired end RNA-Seq so you don't have to delete it anymore when performing a stranded analysis. It also generates the sam header internally, exports unmapped reads, and gzips the output. See http://sourceforge.net/projects/useq/files/USeq_7.9.6.zip/download -cheers, D -- David Austin Nix, PhD Huntsman Cancer Institute Dept. OncSci University of Utah Bioinformatics Shared Resource HCI 3165 (801) 587-4611 dav...@hc... Skype: NextGenBio |
From: James P. <jim...@gm...> - 2011-11-02 19:48:37
|
Hi all, I'm having problems building the splice junction library file, following the isntructions given here: http://useq.sourceforge.net/usageRNASeq.html I'm at the: Create a multi-fasta file containing extended splice junctions matched to your target read length minus 4bp using the USeq MakeTranscriptome app. part Steps one and two go ok. However when I try to run MakeTranscriptome I get lots of errors. Specifically: Error parsing UCSCGeneLine name2 #name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds Error parsing UCSCGeneLine ENSRNOG00000018674 ENSRNOT00000050151 chr1 - 133925529 134302139 133925682 134302088 19 133925529,133932969,133938113,133959565,133978443,133981901,133991271,134081434,134169351, 134170342,134172615,134178756,134179501,134180032,134181232,134196669,134237566,134238370,134301840, 133925868,133933128,133938155,133959640,133978687,133982074,133991402,134081623,134169454,134170407,1341 72639,134179053,134179643,134180175,134181390,134196738,134237638,134238445,134302139, repeated .... I also get to stderr: java.lang.NumberFormatException: For input string: "strand" at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:481) at java.lang.Integer.parseInt(Integer.java:514) at util.bio.parsers.UCSCGeneLine.<init>(UCSCGeneLine.java:62) at util.bio.parsers.UCSCGeneModelTableReader.parseGeneTableFile(UCSCGeneModelTableReader.java:335) at util.bio.parsers.UCSCGeneModelTableReader.<init>(UCSCGeneModelTableReader.java:38) at util.bio.seq.MakeTranscriptome.processArgs(MakeTranscriptome.java:548) at util.bio.seq.MakeTranscriptome.<init>(MakeTranscriptome.java:33) at util.bio.seq.MakeTranscriptome.main(MakeTranscriptome.java:514) repeated ....... which seems strange, it seems as though it doesn't like the - or + perhaps? Anyone seen this error before? Many thanks in advance for any help you can give. The command I am running is: java -jar ../../progs/USeq_7.9.5/Apps/MakeTranscriptome -f ../rat/genome_fastas/ -u ../genetabs/geneTable.PSC.xls -r 30 1> stdout.txt 2> stderr.txt Jim |
From: David N. <dav...@gm...> - 2011-11-02 16:54:02
|
Hello Folks, Given all the headaches associated with BAM files, I've depreciated the Bam2Bar app and replaced it with Sam2USeq for generating read depth coverage tracks. Options are available for creating stranded and relative graphs. The SAM file don't need to be sorted nor have a header. Multiple SAM files will be merged. This app should solve some of the out of memory issues with huge alignment files. The USeq_7.9.5 release is available from https://sourceforge.net/projects/useq/ The xxx.useq graphs can be viewed directly in IGB or converted to wig files with the USeq2Text app, or bigWig files with the USeq2UCSCBig app. If you post your xxx.useq graphs to GenoPub (http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2 ) you can visualize your data in both IGB and the UCSC Genome Browser. -cheers, D |
From: David N. <dav...@gm...> - 2011-10-26 18:44:47
|
Yes, that explains it. The MRSS only provides two scores per window unlike ScanSeqs so you need to adjust what the indexes are. In this case use '-I 0,1 -s 20,1' to threshold 20 (0.01) for the FDR and 1 for the log2Ratio. With one replica though you will get a very conservative estimation of FDR from DESeq (this is what MRSS uses), thus I'd suggest reducing the stringency to 10 or 8. -cheers, D On 10/26/11 9:32 AM, "Baker, Richard" <Ric...@um...> wrote: >*********** 10/26/2011 11:07:34 AM *********** >java -Xmx7G -jar /Applications/USeq_7.9.3/Apps/EnrichedRegionMaker -f >/Users/bakerr/Desktop/Useq/MRSS2/binaryWindowData.swi.zip -t >/Users/bakerr/Desktop/Useq/s2s7ChIPSeq/DupFiltPointData/TreatmentPointData >/Rep0 -c >/Users/bakerr/Desktop/Useq/s2s7ChIPSeq/DupFiltPointData/ControlPointData/R >ep0 > > >Launching... >Looking up indexes... > >Please enter one or more of the score indexes from below: > 0 FDR > 1 Log2((sumT+1)/(sumC+1)) > >It looks as if the xxx.swi file contains only FDR and log2() information >and I gave ERM three criteria to check. Running with -i 1 -s 2 worked >fine. Thanks for the help. > >I only recently discovered USeq. I've been using MACS and PeakSeq for >peak calling (they give essentially the same results), and I probably >won't change now that we're 90% finished with our analyses. However, >I've already found many of USeq's other programs extremely useful and >easy to use (I've been using the GUI Wrapper on my iMac with 8G RAM). >Thanks for making them available! > >************************************************* >Richard Baker, PhD >Department of Microbiology and Physiological Systems >UMass Medical School >55 Lake Avenue N. >Worcester, MA 01655 >508-856-6046 > >On Oct 26, 2011, at 10:40 AM, David Nix wrote: > >> Hello Richard, >> >> Would you mind running the app without the -s and -I options and have it >> print out the indexes for this swi file? >> >> "java -Xmx7G -jar /Applications/USeq_7.9.3/Apps/EnrichedRegionMaker -f >> /Users/bakerr/Desktop/Useq/MRSS2/binaryWindowData.swi.zip" >> >> -cheers, D >> >> On 10/25/11 1:45 PM, "Baker, Richard" <Ric...@um...> >>wrote: >> >>> EnrichedRegionMaker consistently throws the following error when I try >>>to >>> process an xxx.swi file produced by MultipleReplicaScanSeqs: >>> >>> *********** 10/25/2011 03:30:37 PM *********** >>> java -Xmx7G -jar /Applications/USeq_7.9.3/Apps/EnrichedRegionMaker -f >>> /Users/bakerr/Desktop/Useq/MRSS2/binaryWindowData.swi.zip -s 20,20,1 -i >>> 1,2,4 -t >>> >>>/Users/bakerr/Desktop/Useq/s2s7ChIPSeq/DupFiltPointData/TreatmentPointDa >>>ta >>> /Rep0 -c >>> >>>/Users/bakerr/Desktop/Useq/s2s7ChIPSeq/DupFiltPointData/ControlPointData >>>/R >>> ep0 >>> >>> >>> Launching... >>> 25 Sub Window Size >>> >>> Processing binaryWindowData.swi.zip... >>> 400 Max gap >>> >>> Error: max score index is greater than the number of scores! >>> >>> ERM runs fine if called through ChIPSeq using the raw alignment files. >>> What's up? >>> >>> >>>------------------------------------------------------------------------ >>>-- >>> ---- >>> The demand for IT networking professionals continues to grow, and the >>> demand for specialized networking skills is growing even more rapidly. >>> Take a complimentary Learning@Cisco Self-Assessment and learn >>> about Cisco certifications, training, and career opportunities. >>> http://p.sf.net/sfu/cisco-dev2dev >>> _______________________________________________ >>> Useq-users mailing list >>> Use...@li... >>> https://lists.sourceforge.net/lists/listinfo/useq-users >> >> > > |
From: David N. <dav...@gm...> - 2011-10-26 14:46:31
|
Yes, you just need to create a UCSC refflat formatted transcript and gene table (tab delimited: geneName, transcriptName, chrom, strand, transcriptStart, transcriptEnd, codingSeqStart, codingSeqEnd, exonCount, exonStarts(comma delimited), exonEnds), interbase coordinates. The gene table is made by merging the transcript table using the MergeUCSCGeneTable app. See http://useq.sourceforge.net/usageRNASeq.html -cheers, D On 10/25/11 8:29 PM, "Youngman, Elaine" <Ela...@um...> wrote: >Hello all, > >Is it possible to use USeq for genomes other than those in UCSC? I'm >trying to use it with C. elegans data, and the UCSC version of the genome >is much older than the version I am using for all of my other analysis. > >Thanks! >Elaine > > > >-------------------------------------------------------------------------- >---- >The demand for IT networking professionals continues to grow, and the >demand for specialized networking skills is growing even more rapidly. >Take a complimentary Learning@Cisco Self-Assessment and learn >about Cisco certifications, training, and career opportunities. >http://p.sf.net/sfu/cisco-dev2dev >_______________________________________________ >Useq-users mailing list >Use...@li... >https://lists.sourceforge.net/lists/listinfo/useq-users |
From: David N. <dav...@gm...> - 2011-10-26 14:42:55
|
So no control sample? You can convert to PointData and run the DefinedRegionScanSeqs and ScanSeqs with just one sample to get read counts but there are no confidence calls made here. See http://useq.sourceforge.net/usage.html -cheers, D From: Myrto Kostadima <kos...@gm...> Date: Mon, 24 Oct 2011 17:10:36 +0100 To: <use...@li...> Subject: [Useq-users] RNA-seq data - Identification of enriched regions Hi, I have RNA-seq data (76bp paired-end) of a single cell type and would like to identify regions that are transcribed but are not annotated (e.g. novel exons). My alignments are in BAM format and come from GSNAP. Can I perform such analysis using USeq? Any help would be much appreciated. Thanks, M -- Myrto Areti Kostadima EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK ---------------------------------------------------------------------------- -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev___________________________________________ ____ Useq-users mailing list Use...@li... https://lists.sourceforge.net/lists/listinfo/useq-users |
From: David N. <dav...@gm...> - 2011-10-26 14:40:58
|
Hello Richard, Would you mind running the app without the -s and -I options and have it print out the indexes for this swi file? "java -Xmx7G -jar /Applications/USeq_7.9.3/Apps/EnrichedRegionMaker -f /Users/bakerr/Desktop/Useq/MRSS2/binaryWindowData.swi.zip" -cheers, D On 10/25/11 1:45 PM, "Baker, Richard" <Ric...@um...> wrote: >EnrichedRegionMaker consistently throws the following error when I try to >process an xxx.swi file produced by MultipleReplicaScanSeqs: > >*********** 10/25/2011 03:30:37 PM *********** >java -Xmx7G -jar /Applications/USeq_7.9.3/Apps/EnrichedRegionMaker -f >/Users/bakerr/Desktop/Useq/MRSS2/binaryWindowData.swi.zip -s 20,20,1 -i >1,2,4 -t >/Users/bakerr/Desktop/Useq/s2s7ChIPSeq/DupFiltPointData/TreatmentPointData >/Rep0 -c >/Users/bakerr/Desktop/Useq/s2s7ChIPSeq/DupFiltPointData/ControlPointData/R >ep0 > > >Launching... >25 Sub Window Size > >Processing binaryWindowData.swi.zip... > 400 Max gap > >Error: max score index is greater than the number of scores! > >ERM runs fine if called through ChIPSeq using the raw alignment files. >What's up? > >-------------------------------------------------------------------------- >---- >The demand for IT networking professionals continues to grow, and the >demand for specialized networking skills is growing even more rapidly. >Take a complimentary Learning@Cisco Self-Assessment and learn >about Cisco certifications, training, and career opportunities. >http://p.sf.net/sfu/cisco-dev2dev >_______________________________________________ >Useq-users mailing list >Use...@li... >https://lists.sourceforge.net/lists/listinfo/useq-users |
From: Youngman, E. <Ela...@um...> - 2011-10-26 02:30:10
|
Hello all, Is it possible to use USeq for genomes other than those in UCSC? I'm trying to use it with C. elegans data, and the UCSC version of the genome is much older than the version I am using for all of my other analysis. Thanks! Elaine |
From: Baker, R. <Ric...@um...> - 2011-10-25 21:46:03
|
EnrichedRegionMaker consistently throws the following error when I try to process an xxx.swi file produced by MultipleReplicaScanSeqs: *********** 10/25/2011 03:30:37 PM *********** java -Xmx7G -jar /Applications/USeq_7.9.3/Apps/EnrichedRegionMaker -f /Users/bakerr/Desktop/Useq/MRSS2/binaryWindowData.swi.zip -s 20,20,1 -i 1,2,4 -t /Users/bakerr/Desktop/Useq/s2s7ChIPSeq/DupFiltPointData/TreatmentPointData/Rep0 -c /Users/bakerr/Desktop/Useq/s2s7ChIPSeq/DupFiltPointData/ControlPointData/Rep0 Launching... 25 Sub Window Size Processing binaryWindowData.swi.zip... 400 Max gap Error: max score index is greater than the number of scores! ERM runs fine if called through ChIPSeq using the raw alignment files. What's up? |
From: Myrto K. <kos...@gm...> - 2011-10-24 16:10:46
|
Hi, I have RNA-seq data (76bp paired-end) of a single cell type and would like to identify regions that are transcribed but are not annotated (e.g. novel exons). My alignments are in BAM format and come from GSNAP. Can I perform such analysis using USeq? Any help would be much appreciated. Thanks, M -- Myrto Areti Kostadima EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK |
From: David N. <dav...@gm...> - 2011-10-18 15:38:33
|
Could you send your command-line as well as a txt file containing a bit of the input files (head input.txt > subInput.txt or gunzip c input.txt.gz | head > subInput.txt if gzipped)? I suspect the Tag2Point app is parsing on white space and your number of columns is getting collapsed so that the strand column is actually one less. -cheers, David From: Radhouane Aniba <ar...@gm...> Date: Tue, 18 Oct 2011 10:41:55 -0400 To: David Nix <dav...@gm...> Cc: <use...@li...> Subject: Re: [Useq-users] R environment Thank you David, It works but generated a bug I dont understand it, sorry I am just starting using it : Parsing PointData from raw alignments... Parsing treatment PointData... /fs/sh-data/USeq/Data/DNAse/RESULTS/PointData/TreatmentPointData/Rep0 java.lang.ArrayIndexOutOfBoundsException: 5 at edu.utah.seq.parsers.Tag2Point.splitBedFilesToTemp(Tag2Point.java:206) at edu.utah.seq.parsers.Tag2Point.<init>(Tag2Point.java:76) at edu.utah.seq.analysis.ChIPSeq.parsePointData(ChIPSeq.java:306) at edu.utah.seq.analysis.ChIPSeq.parsePointData(ChIPSeq.java:236) at edu.utah.seq.analysis.ChIPSeq.<init>(ChIPSeq.java:73) at edu.utah.seq.analysis.ChIPSeq.main(ChIPSeq.java:449) My Input files are in this format : chr1 161 181 250 + chr1 164 184 250 + chr1 237 257 333 + Thanks Radhouane 2011/10/18 Radhouane Aniba <ar...@gm...> > I am using the Chip-seq app will take a look at its options. > > Radhouane > > > 2011/10/18 David Nix <dav...@gm...> >> Hello Radhouane, >> >> I believe each of the apps that use R have a r option that lets you specify >> where R is? Which app were you trying to run? Did you take a look at the >> command line options (launch the app with no arguments). -cheers, D >> >> >> >> From: Radhouane Aniba <ar...@gm...> >> Date: Tue, 18 Oct 2011 10:18:06 -0400 >> To: <use...@li...> >> Subject: [Useq-users] R environment >> >> Hello everyone, >> >> Is there any option with USeq where we can specify the location of R >> binaries, I am working on a server on which I have no permission to change R, >> so I installed R-2.13.0 in a different folder made my setenv changes but I >> have an error message saying : >> >> Cannot find or execute the R application -> /usr/bin/R >> >> Any help ? >> >> Thanks >> >> Radhouane >> >> >> ----------------------------------------------------------------------------- >> - All the data continuously generated in your IT infrastructure contains a >> definitive record of customers, application performance, security threats, >> fraudulent activity and more. Splunk takes this data and makes sense of it. >> Business sense. IT sense. Common sense. >> http://p.sf.net/sfu/splunk-d2d-oct___________________________________________ >> ____ Useq-users mailing list >> Use...@li...https://lists.sourceforge.net/lists/listinfo/ >> useq-users > > > > -- > Radhouane Aniba > Bioinformatics Postdoctoral Research Scientist > Institute for Advanced Computer Studies > Center for Bioinformatics and Computational Biology (CBCB) > University of Maryland, College Park > MD 20742 > -- Radhouane Aniba Bioinformatics Postdoctoral Research Scientist Institute for Advanced Computer Studies Center for Bioinformatics and Computational Biology (CBCB) University of Maryland, College Park MD 20742 |
From: David N. <Dav...@hc...> - 2011-10-18 15:35:19
|
Yes, that is correct. The minimum reads is used to reduce the number of windows passed to DESeq. This doesn't hurt the sensitivity though since that few reads, even 10:0 treat:cont won't be significant after applying a multiple testing correction. Yes, you can take each dataset (chIP or input) and run ScanSeqs in single dataset mode, don't provide a control, just treatment. Then run the EnrichedRegionMaker and threshold based on the number of reads (e.g. "-s 10, -I 0" for min 10 reads in a window. The output contains an egr file (chr start stop …) for all of the regions with 10 or more reads. Then sum the length of the regions and divide by your genome length * 0.8 (~80% of higher eukaryotic genomes can be mapped). -cheers, D From: Gareth Wilson <gar...@ca...<mailto:gar...@ca...>> Date: Tue, 18 Oct 2011 09:19:35 -0600 To: David Nix <dav...@hc...<mailto:dav...@hc...>> Subject: Proportion of genome analysed? Hi David, I'm using MultipleReplicaScanSeqs on MeDIP cohorts with –m = 10. As far as I gather, each window is tested to see if the total read count is greater or equal to the threshold and, if so, is passed to DESeq to be tested for differential counts. Do you have a method for determining what proportion of the total genome is covered at the required threshold? Many Thanks, Gareth. ------ Dr Gareth A Wilson Bioinformatician Medical Genomics Group UCL Cancer Institute Paul O'Gorman Building University College London 72 Huntley Street London WC1E 6BT tel: +44 (0) 20 7679 0999 ------ |
From: Radhouane A. <ar...@gm...> - 2011-10-18 14:44:13
|
Thank you David, It works but generated a bug I dont understand it, sorry I am just starting using it : Parsing PointData from raw alignments... Parsing treatment PointData... /fs/sh-data/USeq/Data/DNAse/RESULTS/PointData/TreatmentPointData/Rep0 java.lang.ArrayIndexOutOfBoundsException: 5 at edu.utah.seq.parsers.Tag2Point.splitBedFilesToTemp(Tag2Point.java:206) at edu.utah.seq.parsers.Tag2Point.<init>(Tag2Point.java:76) at edu.utah.seq.analysis.ChIPSeq.parsePointData(ChIPSeq.java:306) at edu.utah.seq.analysis.ChIPSeq.parsePointData(ChIPSeq.java:236) at edu.utah.seq.analysis.ChIPSeq.<init>(ChIPSeq.java:73) at edu.utah.seq.analysis.ChIPSeq.main(ChIPSeq.java:449) My Input files are in this format : chr1 161 181 250 + chr1 164 184 250 + chr1 237 257 333 + Thanks Radhouane 2011/10/18 Radhouane Aniba <ar...@gm...> > I am using the Chip-seq app will take a look at its options. > > Radhouane > > > 2011/10/18 David Nix <dav...@gm...> > >> Hello Radhouane, >> >> I believe each of the apps that use R have a –r option that lets you >> specify where R is? Which app were you trying to run? Did you take a look >> at the command line options (launch the app with no arguments). -cheers, D >> >> >> >> From: Radhouane Aniba <ar...@gm...> >> Date: Tue, 18 Oct 2011 10:18:06 -0400 >> To: <use...@li...> >> Subject: [Useq-users] R environment >> >> Hello everyone, >> >> Is there any option with USeq where we can specify the location of R >> binaries, I am working on a server on which I have no permission to change >> R, so I installed R-2.13.0 in a different folder made my setenv changes but >> I have an error message saying : >> >> Cannot find or execute the R application -> /usr/bin/R >> >> Any help ? >> >> Thanks >> >> Radhouane >> >> >> ------------------------------------------------------------------------------ >> All the data continuously generated in your IT infrastructure contains a >> definitive record of customers, application performance, security threats, >> fraudulent activity and more. Splunk takes this data and makes sense of it. >> Business sense. IT sense. Common sense. >> http://p.sf.net/sfu/splunk-d2d-oct_______________________________________________Useq-users mailing list >> Use...@li... >> https://lists.sourceforge.net/lists/listinfo/useq-users >> > > > > -- > *Radhouane Aniba* > *Bioinformatics Postdoctoral Research Scientist* > *Institute for Advanced Computer Studies > Center for Bioinformatics and Computational Biology* *(CBCB)* > *University of Maryland, College Park > MD 20742* > > -- *Radhouane Aniba* *Bioinformatics Postdoctoral Research Scientist* *Institute for Advanced Computer Studies Center for Bioinformatics and Computational Biology* *(CBCB)* *University of Maryland, College Park MD 20742* |
From: Radhouane A. <ar...@gm...> - 2011-10-18 14:24:40
|
I am using the Chip-seq app will take a look at its options. Radhouane 2011/10/18 David Nix <dav...@gm...> > Hello Radhouane, > > I believe each of the apps that use R have a –r option that lets you > specify where R is? Which app were you trying to run? Did you take a look > at the command line options (launch the app with no arguments). -cheers, D > > > > From: Radhouane Aniba <ar...@gm...> > Date: Tue, 18 Oct 2011 10:18:06 -0400 > To: <use...@li...> > Subject: [Useq-users] R environment > > Hello everyone, > > Is there any option with USeq where we can specify the location of R > binaries, I am working on a server on which I have no permission to change > R, so I installed R-2.13.0 in a different folder made my setenv changes but > I have an error message saying : > > Cannot find or execute the R application -> /usr/bin/R > > Any help ? > > Thanks > > Radhouane > > > ------------------------------------------------------------------------------ > All the data continuously generated in your IT infrastructure contains a > definitive record of customers, application performance, security threats, > fraudulent activity and more. Splunk takes this data and makes sense of it. > Business sense. IT sense. Common sense. > http://p.sf.net/sfu/splunk-d2d-oct_______________________________________________Useq-users mailing list > Use...@li... > https://lists.sourceforge.net/lists/listinfo/useq-users > -- *Radhouane Aniba* *Bioinformatics Postdoctoral Research Scientist* *Institute for Advanced Computer Studies Center for Bioinformatics and Computational Biology* *(CBCB)* *University of Maryland, College Park MD 20742* |
From: David N. <dav...@gm...> - 2011-10-18 14:23:02
|
Hello Radhouane, I believe each of the apps that use R have a r option that lets you specify where R is? Which app were you trying to run? Did you take a look at the command line options (launch the app with no arguments). -cheers, D From: Radhouane Aniba <ar...@gm...> Date: Tue, 18 Oct 2011 10:18:06 -0400 To: <use...@li...> Subject: [Useq-users] R environment Hello everyone, Is there any option with USeq where we can specify the location of R binaries, I am working on a server on which I have no permission to change R, so I installed R-2.13.0 in a different folder made my setenv changes but I have an error message saying : Cannot find or execute the R application -> /usr/bin/R Any help ? Thanks Radhouane ---------------------------------------------------------------------------- -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct__________________________________________ _____ Useq-users mailing list Use...@li... https://lists.sourceforge.net/lists/listinfo/useq-users |
From: Radhouane A. <ar...@gm...> - 2011-10-18 14:18:32
|
Hello everyone, Is there any option with USeq where we can specify the location of R binaries, I am working on a server on which I have no permission to change R, so I installed R-2.13.0 in a different folder made my setenv changes but I have an error message saying : Cannot find or execute the R application -> /usr/bin/R Any help ? Thanks Radhouane |
From: David N. <dav...@gm...> - 2011-10-17 20:49:30
|
Hello Radhouane, Take a look at the user guide. It details what data format (PointData) is needed for running these apps. http://useq.sourceforge.net/usage.html -cheers, D From: Radhouane Aniba <ar...@gm...> Date: Mon, 17 Oct 2011 08:33:25 -0700 To: <use...@li...> Subject: [Useq-users] USeq Input Question Hello USeq users, I am new to this package, I am giving it a try but some information are not that clear for me. I am interested in the app MultiplReplicateScanSeqs for Chip-Seq data analysis and reading the documentation I noticed that example java -Xmx4G -jar pathTo/USeq/Apps/ScanSeqs -t /Data/PolIIRep1/,/Data/PolIIRep2/ -c /Data/Input1/,Data/Input2/ -s /Data/PolIIResults -w 200 -p 100 -f -g 5 Although it looks obvious, there is no indication on the input format, what kind of input format this program uses, I have replicates input as bed files, and a single Input file for both of them Thanks for your help Radhouane ---------------------------------------------------------------------------- -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct__________________________________________ _____ Useq-users mailing list Use...@li... https://lists.sourceforge.net/lists/listinfo/useq-users |
From: Radhouane A. <ar...@gm...> - 2011-10-17 15:34:29
|
Hello USeq users, I am new to this package, I am giving it a try but some information are not that clear for me. I am interested in the app MultiplReplicateScanSeqs for Chip-Seq data analysis and reading the documentation I noticed that example java -Xmx4G -jar pathTo/USeq/Apps/ScanSeqs -t /Data/PolIIRep1/,/Data/PolIIRep2/ -c /Data/Input1/,Data/Input2/ -s /Data/PolIIResults -w 200 -p 100 -f -g 5 Although it looks obvious, there is no indication on the input format, what kind of input format this program uses, I have replicates input as bed files, and a single Input file for both of them Thanks for your help Radhouane |
From: David N. <Dav...@hc...> - 2011-07-20 22:47:28
|
Hello Folks, I wrote up some instructions for how to take advantage of the reworked RNA-Seq apps in Useq. The approach here is different than what most other RNA-Seq analysis entail. Alignments are made to genome fastas plus splice junctions that, when needed, span multiple exons. This includes all known splice junctions as well as all theoretical splice junction combinations. Thus junction matches are biased toward aligning to known annotation instead of the closest partial match as Tophat and other seed and extend algorithms employ. This avoids a common problem of creating apparent novel exons inside intronic regions. As before, I'm leaning heavily on Anders' DESeq package for calling differential expression since it controls for overdispersion in the count data with a negative binomial test. Gone are the days of not running biological replicas. 3-4 are mandatory for each condition. http://useq.sourceforge.net/usageRNASeq.html This is included in the Documentation folder in the Useq download from SourceForge. There are three key improvements with this reworking: 1. It supports any length of sequence reads, the prior version was designed to work with 36bp reads, 50bp and 101 bp reads would often only partially align to splice junctions. 2. It uses BAM alignments as the working raw data format enabling collection and analysis of the underlying sequence data as well as the structure of the splice junction matches to better call differential splicing. The use of BAM files also enables users to take advantage of external apps for analysis and visualization. 3. Depth of coverage tracks now accurately map splice junction reads across multiple exons. I'll be building support for these apps into the RNASeq wrapper and depreciating the old methods. -cheers, D -- David Austin Nix, PhD Research Assistant Professor in Oncological Sciences Bioinformatics Shared Resource Huntsman Cancer Institute and the University of Utah 2000 Circle of Hope, Salt Lake City, UT 84112 (801) 587-4611 Room HCI 3165 dav...@hc... http://bioserver.hci.utah.edu |