Activity for Congting Ye
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Congting Ye posted a comment on discussion General Discussion
Hi Hugo, Our APAtrap pipeline does not currently support parallel computing. One way to speed up the process is, as you mentioned, to separate bedgraph files and gene model file based on their genomic positions, and process them separately and/or simultaneously. Since the result for each gene corresponds to only one line in the output file, you can use the "cat" command line tool to combine them. Best, Congting
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Hi Marie, It's clear that you used an incorrect gene model file, the gene model file should be in bed12 format. You could go to this link http://genome.ucsc.edu/FAQ/FAQformat#format1manual for details, and go to the user manual page to see how to make a suitble gene model file from GTF file of genome annotation. Congting Ye
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Hi Andrew, It would be better that you could send me the ICF.APA.txt file for figuring out the problem. Congting
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This is a normal prompt, indicating there is a region with noncontinuous coverage of reads.
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Hi Thomas, Thanks for your suggestions, I have added a sentence in the user mannual and ReadMe.md to specify that APAtrap follows specifications on website (http://creativecommons.org/licenses/by-nc-sa/3.0/). Hope this works! Best, Congting
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Hi Yue, It seems that the program cannot locate the file 'hg19.utr.bed' in the working directory 'C:\Users\lenovo\Documents'. Please make sure the file name and location you typed are correct. Is there any special character in your file name, such as space? Congting Ye
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Hi Yao-Chung, I have run the APAtrap with the annotation bed file downloaded from the above link and the test data (https://sourceforge.net/projects/apatrap/files/Test_Data.zip/download), and find out it could run successfully, could you check if there is anything wrong with your bedgraph file? The source code of APAtrap could be find at this website (https://sourceforge.net/projects/apatrap/files/Source%20Codes/). Congting Ye
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Hi Yao-Chung, You used an incorrect annotation bed file in identifyDistal3UTR, you could find a correct annotation bed file from this link http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=787774005_ABQYAdCOlXgJmK8wIcJqn5Hwc2ad&clade=mammal&org=Human&db=hg38&hgta_group=genes&hgta_track=refSeqComposite&hgta_table=refGene&hgta_regionType=genome&position=chr1%3A11%2C102%2C837-11%2C267%2C747&hgta_outputType=bed&hgta_outFileName=test.txt Congting Ye
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At the line 7 and 8 of the detectIR_Demo, outputFile = './Result/detectIR.TAIR10.perfect.fasta'; runtimeFile = './Result/detectIR.TAIR10.perfect.runtime'; you should make sure the folder 'Result' already exists or change it to outputFile = './detectIR.TAIR10.perfect.fasta'; runtimeFile = './detectIR.TAIR10.perfect.runtime';
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Hi Peter, It would be great that you could send me the annotation and coverage files for figuring out the problem. My email address is yec@xmu.edu.cn. Congting Ye
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Separate_Exp includes the expression levels of each APA sites (from the most proximal site to the distal site, seperated by comma). By the way, please post your comments in the Discussion page of the APAtrap project if you have any new questions. Congting Ye
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The 'Predicted_APA' only indicates the coordinates of proximal APA sites inferred by the 'predictAPA' step of APAtrap, and the distal APA site is the end the 3' UTR region and is showed in the 'Loci' coloumn. So the number of values in 'Separate_Exp' is always 1 more than the number of values in 'Predicted_APA'. Hope this helps, Congting Ye
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In your case, this indicates that no candidate MITEs was detected from your input. I guess that you may run detectMITE using a small fasta file for test, a small input often results in nothing detected. You could run detectMITE with Arabidopsis genome to test whether it could run correctly. Thanks for your interest in detectMITE!
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Hi Virginia Markham, According to the error info you post, I figure out that you were using an old version of detectMITE. The code "Cluster = fastaread(['./result/' genome '.clusteredCandidateTE' num2str(count) '.fasta.clstr']);" is at line 60 of the old verion (such as detectMITE.20160818.tar.gz), but at line 62 of the newest version. Please go the link (https://sourceforge.net/projects/detectmite/files/detectMITE.20170425.tar.gz/download) to download the newest version. Error using fastaread (line...
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Hi Nik dAK, (1) The input -u in step 3.2 refer to the output of 3.1. (2) The APAtrap does not support multithreading currently. One possible way to speed up your process is to divide you sample data by chromosome, and then run the divided data separately. Congting Ye
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Hi Thomas, It seems that you built your own gene model file from a gff/gtf annotation file, not downloaded it from the UCSC Table Browser. Could you please send me your gene model file and a part of your bedgraph file witch covers the regions of genes you mentioned, it will be helpful for me to figure out the problem (I assumed the error was caused by a wrong gene model file). Best, Congting Ye
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Hi Thomas, Thanks for your interest in APAtrap! For we often generate several biological replicates of a treatment/condition in experiments, the 'number of groups' in APAtrap is used to represent 'the number of treatments/conditions' in one study. You can use the '–g' parameter to set the number of groups (treatment/condition) of your input files, and use the '–n' parameter to set the number of biological replicates in each group. For example, -g 3 -n 1 2 3 Indicates there are 6 input files divided...
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Hi Haifeng, There is no error in the gene model file 'hg19.genemodel.bed'. The 'NA' is caused from that you did not provide a gene symbol file in the step of identifyDistal3UTR using parameter '-s'. The content of a gene symbol file should be like as follows, gene_id gene_name NM_001198993 NADK NM_017900 AURKAIP1 NM_001014980 FAM132A NM_001198994 NADK NM_003820 TNFRSF14 NM_003036 SKI NM_001242672 TTC34 NM_152492 CCDC27 Thanks for your interest in APAtrap! Congting Ye
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