From: Alec W. <al...@br...> - 2011-05-26 18:31:47
|
Right, sorry. -Alec On 5/26/11 2:25 PM, mei ge wrote: > Hi Alec, > The Homo_sapiens_assembly19.rRNA.interval_list has 85 sequences, my > bam file has 25 sequences. I need to edit your file to match the bam > sequences. > Thanks > Robin > > > --- On *Thu, 5/26/11, Alec Wysoker /<al...@br...>/* wrote: > > > From: Alec Wysoker <al...@br...> > Subject: Re: [Samtools-help] Picard release 1.46 > To: "mei ge" <rge...@ya...> > Cc: "Sam...@li..." > <Sam...@li...> > Date: Thursday, May 26, 2011, 2:18 PM > > Hi Robin, > > I will improve this error message so it is clearer. > Homo_sapiens_assembly19.rRNA.interval_list has 25 sequences, and > s_1_2_pefca_2_sorted.bam has 85. You may need to edit the > interval list so that it has all the sequences in your bam, and > uses the same naming convention. > > -Alec > > On 5/26/11 2:09 PM, mei ge wrote: >> Hi Alec: >> I used your ribosomal interval file and I got an error as follow: >> [Thu May 26 13:50:45 EDT 2011] >> net.sf.picard.analysis.CollectRnaSeqMetrics >> REF_FLAT=/home/gtf/hg19/refFlat_table_for_picard.txt >> RIBOSOMAL_INTERVALS=/home/gtf/ribosomal_RNA/Homo_sapiens_assembly19.rRNA.interval_list >> STRAND_SPECIFICITY=NONE >> INPUT=/s_1_2_pefca_2/s_1_2_pefca_2_sorted.bam >> OUTPUT=/s_1_2_pefca_2/s_1_2_pefca_2_RNAseq_metrics.txt >> REFERENCE_SEQUENCE=/databases/hs_chromosomes/hg19.fa >> ASSUME_SORTED=true >> VALIDATION_STRINGENCY=SILENT >> STOP_AFTER=0 >> VERBOSITY=INFO >> QUIET=false >> COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false >> CREATE_MD5_FILE=false >> INFO 2011-05-26 13:50:46 CollectRnaSeqMetrics Loaded 21987 genes. >> [Thu May 26 13:50:46 EDT 2011] >> net.sf.picard.analysis.CollectRnaSeqMetrics done. Elapsed time: >> 0.03 minutes. >> Runtime.totalMemory()=165347328 >> Exception in thread "main" >> net.sf.samtools.util.SequenceUtil$SequenceListsDifferException: >> Sequence dictionaries are not the same size (25, 85) >> at >> net.sf.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil.java:84) >> at >> net.sf.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:126) >> at >> net.sf.picard.analysis.CollectRnaSeqMetrics.setup(CollectRnaSeqMetrics.java:86) >> at >> net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:101) >> at >> net.sf.picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:54) >> at >> net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:158) >> at >> net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:118) >> at >> net.sf.picard.analysis.CollectRnaSeqMetrics.main(CollectRnaSeqMetrics.java:77) >> >> >> --- On *Thu, 5/26/11, Alec Wysoker /<al...@br...> >> <http://us.mc388.mail.yahoo.com/mc/compose?to=al...@br...>/* >> wrote: >> >> >> From: Alec Wysoker <al...@br...> >> <http://us.mc388.mail.yahoo.com/mc/compose?to=al...@br...> >> Subject: Re: [Samtools-help] Picard release 1.46 >> To: "mei ge" <rge...@ya...> >> <http://us.mc388.mail.yahoo.com/mc/compose?to=rge...@ya...> >> Cc: "Sam...@li..." >> <http://us.mc388.mail.yahoo.com/mc/compose?to=Sam...@li...> >> <Sam...@li...> >> <http://us.mc388.mail.yahoo.com/mc/compose?to=Sam...@li...> >> Date: Thursday, May 26, 2011, 10:58 AM >> >> Hi Robin, >> >> Human HG19 is attached. I don't have one for mouse. I just >> extracted these from gencode GTF file. Presumably you could >> do the same for mouse. Interval list format described here: >> http://picard.sourceforge.net/javadoc/net/sf/picard/util/IntervalList.html >> >> Note that this file is not required by CollectRnaSeqMetrics, >> but if you do not provide it the program will not be able to >> determine when reads map to rRNA. >> >> -Alec >> >> On 5/26/11 9:54 AM, mei ge wrote: >>> Hi Alec: >>> I am looking for human (hg19) and mouse(mm9). >>> Thanks >>> Robin >>> >>> --- On *Wed, 5/25/11, Alec Wysoker >>> /<al...@br...> >>> <http://us.mc388.mail.yahoo.com/mc/compose?to=al...@br...>/* >>> wrote: >>> >>> >>> From: Alec Wysoker <al...@br...> >>> <http://us.mc388.mail.yahoo.com/mc/compose?to=al...@br...> >>> Subject: Re: [Samtools-help] Picard release 1.46 >>> To: "mei ge" <rge...@ya...> >>> <http://us.mc388.mail.yahoo.com/mc/compose?to=rge...@ya...> >>> Cc: "samtools help" >>> <sam...@li...> >>> <http://us.mc388.mail.yahoo.com/mc/compose?to=sam...@li...> >>> Date: Wednesday, May 25, 2011, 4:52 PM >>> >>> Hi Mei, >>> >>> Are you looking for human? If so, what genome build? >>> >>> -Alec >>> >>> On 5/25/11 3:15 PM, mei ge wrote: >>>> Hi Alec, >>>> I use the CollectRnaSeqMetrics in the new release >>>> Picard. I don't know where to get the >>>> Ribosomal_intervals file. Can you point a place for >>>> the file? >>>> Thanks >>>> Mei >>>> |