single end RNA sequence mapping-TOPHAT- noBAM file?

[ibn.adam]

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.

#!/bin/bash
# usage: qsub -v SAMPLE="name" intestinaltophat1lane.pbs
#PBS -l walltime=100:00:00
#PBS -m ae
#PBS -M [email protected]
### Set the queue name, given to you when you get a reservation.
#PBS -l nodes=1: ppn=8
ROOT=/home/xxx/projects/intestinal/mRNA/
cd $ROOT/$SAMPLE
ROOTB=/home/xxx/tophat_output/intestinal/mRNA/
TOPHATOUTPUT=$ROOTB$SAMPLE
mkdir $TOPHATOUTPUT
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
rm $TOPHATOUTPUT/temp*





please help me in correcting the script.
many thanks,
Adam