Tophat trouble

[gaurav]

Hi there,

I am having trouble with my tophat command for NGS data analysis. The commands I have been using are:

export PATH=/opt/bowtie-0.12.8:$PATH
mkdir bowtie_index
bowtie-build TAIR10.20.dna.toplevel.fa bowtie_index
export PATH=/opt/tophat/bin/:$PATH
export PATH=/opt/samtools-0.1.17/bin:$PATH
tophat -i 40 -I 1000 -G TAIR10.20.gtf -o ./tophat.out_arib3 bowtie_index SRR548277.fastq


The output files I am getting are a fa file, sam file, bam file, and lots of z- files. However, I am not getting any accepted hits or bed files.

I would highly highly appreciate if anyone please help me solving the problem.

Thanks
G

[dpryan]

Did it actually run to completion or did it die at some point? I assume the latter. What are the names of the files that it did create?

[gaurav]

Hi dpryan,

Thanks for your reply.

Tophat is running to complete and the files it is outputting are:

stub_header.sam
practice.fa
practice.bwt.samheader.sam
left_kept_reads_seg4.fq.z
left_kept_reads_seg3.missing.fq.z
left_kept_reads_seg3.fq.z
left_kept_reads_seg3.bwtout.z
left_kept_reads_seg2.missing.fq.z
left_kept_reads_seg2.fq.z
left_kept_reads_seg2.bwtout.z
left_kept_reads_seg1.missing.fq.z
left_kept_reads_seg1.fq.z
left_kept_reads_seg1.bwtout.z
left_kept_reads_missing.fq.z
left_kept_reads.unspl.bam
left_kept_reads.fq.z
left_kept_reads.bwtout.z
24594.bwt_unmapped.z.fifo

Thanks for your help.

[dpryan]

That looks a lot like it aborted before finishing. There's probably a "log" directory or something like that. Have a look at the run log in there to see if you can discern where things stopped.

[gaurav]

Hey dpryan,
You were right, it was just an issue of being stopped in halfway (I was using a cluster for running it and been logged off in between).. Anyways, it ran properly now and got requisite files ..

Thanks for your help again.

G