Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
Tophat for single end reads lynn012 RNA Sequencing 20 10-27-2014 10:04 PM
TopHat -paired end vs single end reads adarshjose RNA Sequencing 10 06-12-2012 07:15 PM
Can paired-end mapping produce more reads than single-end ? warrenemmett Bioinformatics 13 03-21-2012 12:10 AM
RNA-seq: Replicates, single-end, paired-end story pasta Bioinformatics 2 07-05-2011 12:51 AM
BOth single and paired end reads in a file!! adgen Illumina/Solexa 0 06-30-2010 11:28 AM

Thread Tools
Old 10-26-2011, 02:35 PM   #1
Junior Member
Location: USA

Join Date: Aug 2011
Posts: 8
Default single end RNA sequence mapping-TOPHAT- noBAM file?

Dear all,

I am maping one end mRNA sequencing on TOPHAT with human reference genome hg19. From sequencinglab i had got many fastq files that, I have merged to a sequence.txt file. I am using that sequence.txt file to run on TOPHAT for mapping.

The problem is, I am not getting BAM file in TOPHAT output. All i am getting is a hg19.fas file, which i believe is the reference genome file I am using.

I am using following script for TOPHAT.

# usage: qsub -v SAMPLE="name" intestinaltophat1lane.pbs
#PBS -l walltime=100:00:00
#PBS -m ae
### Set the queue name, given to you when you get a reservation.
#PBS -l nodes=1: ppn=8
SEQFILES=`ls *_sequence.txt`
tophat -p 8 -r 50 --microexon-search -G /home/ah644/hg19andhs37/Homo_sapiens.GRCh37.62.gtf --solexa1.3-quals -o $TOPHATOUTPUT /home/ah644/hg19andhs37/hg19 $SEQFILES
coverageBed -abam $TOPHATOUTPUT/accepted_hits.bam -b /home/ah644/hg19andhs37/hg19ensembl.BED > $TOPHATOUTPUT/geneexpression.txt
cut -f 1,2,3,4,13,14,15,16 $TOPHATOUTPUT/geneexpression.txt > $TOPHATOUTPUT/temp
cut -f 5 /home/ah644/hg19andhs37/hg19ensemblgeneinfo.txt > $TOPHATOUTPUT/temp2
paste $TOPHATOUTPUT/temp $TOPHATOUTPUT/temp2 > $TOPHATOUTPUT/reducedgeneexpression.txt

please help me in correcting the script.
many thanks,

Last edited by ibn.adam; 10-28-2011 at 07:51 AM.
ibn.adam 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 10:05 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO