Tophat tool error

Question

[blooming.daisy333]

im using tophat too determine splice junction but encountering a strange error.

[2018-04-16 12:43:28] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-04-16 12:43:28] Checking for Bowtie
                  Bowtie version:        2.2.6.0
[2018-04-16 12:43:28] Checking for Bowtie index files (genome)..
[2018-04-16 12:43:28] Checking for reference FASTA file
[2018-04-16 12:43:28] Generating SAM header for /data/sata4/memona/arboreum_index
Traceback (most recent call last):
  File "./tophat", line 4107, in <module>
    sys.exit(main())
  File "./tophat", line 3961, in main
    params.read_params = check_reads_format(params, reads_list)
  File "./tophat", line 1856, in check_reads_format
    zf = ZReader(f_name, params)
  File "./tophat", line 1809, in __init__
    self.file=open(filename)
IOError: [Errno 2] No such file or directory: ''

Can anyone suggest any solution to this problem

the command im using to align is as follows:

[memona@nibge tophat-2.1.1.Linux_x86_64]$ ./tophat -p 24 /data/sata4/memona/arboreum_index /data/sata4/memona/Trimmomatic-0.36/SRR959590_A_1P.fq, /data/sata4/memona/Trimmomatic-0.36/SRR959590_A_1U.fq, /data/sata4/memona/Trimmomatic-0.36/SRR959590_A_2P.fq, /data/sata4/memona/Trimmomatic-0.36/SRR959590_A_2U.fq

[Pierre Lindenbaum]

do not use tophat:

Please stop using Tophat https://t.co/Es4ohxOEyx Cole and I developed the method in *2008*. It was greatly improved in TopHat2 then HISAT & HISAT2. There is no reason to use it anymore. I have been saying this for years yet it has more citations this year than last #methodsmatter

— Lior Pachter (@lpachter) December 2, 2017

[blooming.daisy333]

im using TopHat (v2.1.1) version.\ is it not tophat2...???

[WouterDeCoster]

TopHat 2.1.1 is TopHat 2, it's just a different subversion. Doesn't change that you should stop using it.

[WouterDeCoster]

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

[WouterDeCoster]

You should know that the old 'Tuxedo' pipeline of Tophat(2) and Cufflinks 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. There are also other alternatives, including alignment with STAR and bbmap, or pseudo-alignment using salmon.

Answer 1

[WouterDeCoster]

In addition to the comments above regarding TopHat, my first guess is that you should remove the spaces in the comma separated list of input files.