Question: Tophat tool error
1
gravatar for blooming.daisy333
10 days ago by
blooming.daisy3330 wrote:

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
next-gen • 73 views
ADD COMMENTlink modified 10 days ago by WouterDeCoster27k • written 10 days ago by blooming.daisy3330
4

do not use tophat:

ADD REPLYlink written 10 days ago by Pierre Lindenbaum106k

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

ADD REPLYlink written 10 days ago by blooming.daisy3330

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

ADD REPLYlink written 10 days ago by WouterDeCoster27k
1

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:

101010 Button

ADD REPLYlink written 10 days ago by WouterDeCoster27k
1

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.

ADD REPLYlink written 10 days ago by WouterDeCoster27k
1
gravatar for WouterDeCoster
10 days ago by
Belgium
WouterDeCoster27k wrote:

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.

ADD COMMENTlink written 10 days ago by WouterDeCoster27k
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