Mapping Step 2 #8
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What is written to stdout and stderr? There might not be an error, but On Mon, Apr 6, 2015 at 1:00 PM, Kimberly notifications@github.com wrote:
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Thank you so much for getting back to me, I greatly appreciate your help! I can not seem to find stderr anywhere. I’ve looked everywhere. Am I supposed to pull it out with a command in terminal because the file doesn’t seem to exist on my computer. I’m sorry I’m not very helpful in resolving the issue. I’m new to this :/ Thank you so much!
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Ah sorry for the confusion. Earlier you sent me what was printed when you On Mon, Apr 6, 2015 at 2:45 PM, Kimberly notifications@github.com wrote:
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I didn’t save it but I didn’t receive an error messages after running step 2 on Mapping and even said Finished! when it was done. My command $ python /Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/find_intersecting_snps.py /Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/NA06894_tophat_out/accepted_hits.bam /Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/SNP_files However my new files to remap are empty
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That is strange. Have you checked to make sure that the SNP files you sent On Mon, Apr 6, 2015 at 3:08 PM, Kimberly notifications@github.com wrote:
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My SNP files are filled and are done correctly with position, ref allele, alt allele each file is ~ 3-20MB and the accepted_hits.keep.bam is 7.7MB
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Do the chr#.snps.txt.gz files need to contain a header? "position RefAllele AltAllele" because my chr# files do not contain a header.
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They shouldn't contain headers. How large was your originally mapped bam? On Mon, Apr 6, 2015 at 3:37 PM, Kimberly notifications@github.com wrote:
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My original mapped bam from running TopHat is 25.7MB
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That is unsorted? The sorted bam files often end up smaller. Are you SNPs On Mon, Apr 6, 2015 at 3:57 PM, Kimberly notifications@github.com wrote:
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I’m sorry I don’t fully understand and I don’t know if my SNPs are sorted or not. I’m confused. Here is my TopHat command $ ./tophat --no-coverage-search -o /Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/NA06894_tophat_out -p 6 -G /Users/olneykimberly/Desktop/1_code/gencode.v18.annotation.gtf /Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/GenomicReference/build37_used_by_cg /Users/olneykimberly/Desktop/TopHat/tophat-2.0.13.OSX_x86_64/ASE_WASP_Files/1000GenomesData/SRR_files/SRR035022.filt.fastq Output files from TopHat:
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I'm trying to get a sense of how many reads are kept after step 2. It On Mon, Apr 6, 2015 at 4:10 PM, Kimberly notifications@github.com wrote:
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Attachments available until May 6, 2015 Here is my accepted_hits.bam. The SNP files are too large to send over all of them so I selected chr13 to send since it’s one of the smaller chromosomes. If you need all of them I’d be happy to send them over I’ll just have to send multiple emails if that’s okay.
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Did you get my data I sent over?
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remove samples argument from bam2h5
The output files are empty but I receive no error message or anything. I have no idea why my accepted_hits.quality.remap.num.gz and remap.fq.gz files are empty
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