tophat alignment error

Question

[hariompraju]

Hi,

I am trying to run tophat alignment, but am unable to do so due to the error shown below:

[2017-03-29 12:45:12] Beginning TopHat run (v2.0.0)
-----------------------------------------------
[2017-03-29 12:45:12] Checking for Bowtie
  Bowtie 2 not found, checking for older version..
                  Bowtie version:        1.1.2.0
[2017-03-29 12:45:12] Checking for Samtools
Traceback (most recent call last):
  File "/apps/tophat-2.0.0.Linux_x86_64/tophat", line 3778, in <module>
    sys.exit(main())
  File "/apps/tophat-2.0.0.Linux_x86_64/tophat", line 3593, in main
    check_samtools()
  File "/apps/tophat-2.0.0.Linux_x86_64/tophat", line 1402, in check_samtools
    samtools_version_str, samtools_version_arr = get_samtools_version()
  File "/apps/tophat-2.0.0.Linux_x86_64/tophat", line 1384, in get_samtools_ve                                                                                          rsion
    samtools_version_arr = [int(version_match.group(x)) for x in [1,2,3]]
AttributeError: 'NoneType' object has no attribute 'group'

Can someone please help me out with this asap. Thank you in advance.

[WouterDeCoster]

Looks like both your tophat installation and bowtie are outdated, so your first reflex should be to update to the latest version and try again. That being said, you should know that Tophat is no longer the "advisable" tool for RNA-seq analysis. The software is deprecated/ in low maintenance and should be replaced by HISAT2, StringTie and ballgown. See this paper: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. (If you can't get access to that publication, let me know and I'll -cough- help you.) There are also other alternatives, including alignment with STAR and bbmap,...

[hariompraju]

Thank you so much for the paper, Sir. It was indeed helpful.