<p>Hi there,</p>

<p>I have ran TopHat successfully with the fusions.out also. But I am unable to understand the directory structure i.e. how to create the directory structure although I have gone through the tutorial but always arising with errors in Tophat fusion.</p>

<p>The created directories are:</p>

<pre><code>./blast_human/human_genomic*, nt* and other_genomic*
tophat_sample11 (containing the output files from TopHat2)
hg19
ensGene.txt
refGene.txt
mcl.txt
./blast/blastall and blastn
</code></pre>

<p>whenever I ran the command:</p>

<pre><code>./tophat-fusion-post -o ./FUSIONOUT --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 hg19
</code></pre>

<p>the error is:</p>

<pre><code>[Mon Jan 21 16:00:55 2013] Beginning TopHat-Fusion post-processing run (v2.0.6)

[Mon Jan 21 16:00:55 2013] Extracting 23-mer around fusions and mapping them using Bowtie
        samples updated

Traceback (most recent call last):
  File "./tophat-fusion-post", line 2091, in ?
    sys.exit(main())

File "./tophat-fusion-post", line 2059, in main
    map_fusion_kmer(bwt_idx_prefix, params, sample_updated)

File "./tophat-fusion-post", line 315, in map_fusion_kmer
    subprocess.call(cmd, stdout=open(output_dir + 'fusion_seq.bwtout', 'w'), stderr=open('/dev/null', 'w'))

  File "/usr/lib64/python2.4/subprocess.py", line 412, in call
    return Popen(*args, **kwargs).wait()

File "/usr/lib64/python2.4/subprocess.py", line 542, in __init__
    errread, errwrite)

File "/usr/lib64/python2.4/subprocess.py", line 975, in _execute_child
    raise child_exception

OSError: [Errno 2] No such file or directory
</code></pre>

<p>No log file is generated.</p>

<p>Thanking in advance!</p>

<p>The error was arising because Bowtie wasn't found in the path. So the path need to be defined as </p>

<p>PATH=$PATH:/path/to/bowtie</p>

<p>It worked for me...</p>
