Error while running Tophat

[koneru_18]

Hi all,

I am new learner of RNA-Seq data analysis and started learning from this paper http://www.ncbi.nlm.nih.gov/pubmed/22383036. The data is drosophila melanogaster paired end.

Tophat version is :TopHat v2.0.9
Bowtie version is : version 2.1.0

When I am running tophat command, I get this error

[2013-10-18 04:24:42] Reading known junctions from GTF file
[2013-10-18 04:24:46] Preparing reads
left reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded)
right reads: min. length=75, max. length=75, 11607353 kept reads (0 discarded)
[2013-10-18 04:28:33] Building transcriptome data files..
[2013-10-18 04:28:50] Building Bowtie index from genes.fa
[2013-10-18 04:36:09] Mapping left_kept_reads to transcriptome genes with Bowtie2
[FAILED]
Error running bowtie:


Can someone help me in this? Any kind of help is appreciated

Thanks in advance.

[dpryan]

You'll have to look in the run log. There, you'll find the actual command that tophat2 was trying to run. Just run that command yourself and you'll receive the underlying error message. Presumably that will be informative.