Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
Tophat: merging accepted_hits.bam and unmapped.bam offspring RNA Sequencing 36 08-13-2015 03:08 AM
Missing accepted_hits.bam and junctions.bed files eriklq Bioinformatics 1 09-26-2013 12:16 PM
tophat problem: no accepted_hits.bam generated RNAer Bioinformatics 9 08-30-2013 09:41 AM
tophat problem: no accepted_hits.bam generated RNAer Bioinformatics 0 07-19-2011 12:18 PM
TOPHAT EMPTY accepted_hits.bam ISSUE waterboy Bioinformatics 1 11-16-2010 08:48 AM

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

Join Date: Apr 2013
Posts: 13
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.

shirley0818 is offline   Reply With Quote
Old 02-03-2014, 05:55 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

It's likely that the process was killed or ran into an error. Look through the log files to find out what went wrong.
dpryan is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 03:57 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO