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Old 02-03-2014, 05:48 AM   #1
shirley0818
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Location: MA

Join Date: Apr 2013
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Default TopHat generates accepted_hits.bam files for some of my samples, but for other

Dear Group,

I have run TopHat 2.0.9 and 2.0.10 for my 75 PE RNA-sequencing data. Totally, I have 8 samples sequenced on each lane on Illumina HiSeq 2000.

My problem is I got accepted_hits.bam results for 5 samples out of 8. For other 3 samples, the .bam files can be only found under "tmp" dir.

Here is the command
$tophat -r 50 --mate-std-dev 70 --keep-tmp --no-coverage-search -o ./tophat_out /Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/genome sample1_R1.fastq.gz sample1_R2.fastq.gz

Any help would be very appreciated.

Shirley
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Old 02-03-2014, 05:55 AM   #2
dpryan
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Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
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It's likely that the process was killed or ran into an error. Look through the log files to find out what went wrong.
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