[maximilianh]

In my case I forgot the -C for colorspace reads. Since bowtie won't run in this case, it will give the same error message. This behavior of tophat really needs to be corrected and the output of bowtie has to be shown on screen.

[maximilianh]

For anyone else who runs into this problem: Get the file logs/run.log from your tophat output directory. Search for the line that starts with bowtie and copy/paste it into a command line. Bowtie will fail and the error message tells you what the problem was.

[maximilianh]

Here is a patch for tophat 1.2.0 that fixes this:
< if not os.path.isfile(unmapped_reads_fasta_name):
< sys.stderr.write("Error: Bowtie results not found, error message from bowtie was:\n")
< logData = open(logging_dir + tmp_fname + ".log").read()
< sys.stderr.write(logData)
< sys.exit(1)
<

[acthegreatp]

Thank you for your post. I fix the problem. I realised that I was using the whole genome itself instead the reads..