TopHat running error ？

[baohua100]

populus@Rust:~/tophat-1.0.9/bin/test_data$ ../tophat -r 20 test_ref reads_1.fq reads_2.fq

[Wed Jul 22 04:03:11 2009] Beginning TopHat run (v1.0.9)
-----------------------------------------------
[Wed Jul 22 04:03:11 2009] Preparing output location ./tophat_out/
[Wed Jul 22 04:03:11 2009] Checking for Bowtie index files
[Wed Jul 22 04:03:11 2009] Checking for reference FASTA file
[Wed Jul 22 04:03:11 2009] Checking for Bowtie
Traceback (most recent call last):
File "../tophat", line 1484, in <module>
sys.exit(main())
File "../tophat", line 1420, in main
check_bowtie()
File "../tophat", line 567, in check_bowtie
bowtie_version = get_bowtie_version()
File "../tophat", line 548, in get_bowtie_version
proc = subprocess.Popen(['bowtie', '--version'],stdout=subprocess.PIPE)
File "/usr/lib/python2.5/subprocess.py", line 594, in __init__
errread, errwrite)
File "/usr/lib/python2.5/subprocess.py", line 1147, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

[Cole Trapnell]

This means that TopHat cannot execute Bowtie on your system, which usually means Bowtie is not in your PATH. Sorry for the unfriendly error message. The upcoming version 1.0.10 gives a friendlier explanation of what happened.

[baohua100]

Thank you. It's OK!

We have paired-end reads. One read is 50bp but the other is 36bp. Can Tophat handle with different length of paired reads?

[baohua100]

If I have 5 singleton reads files , but the read length are 36,36,41,41,50.

tophat ref reads1.fq reads2.fq reads3.fq reads4.fq reads5.fq

can tophat handle this suituation?