TOPHAT error in mapping left_kept_reads step during a mapping with fusion search with bowtie1

Question

[Gabriel Wajnberg]

I am trying to use tophat with single end fastq for fusion search. I got the bowtie indexes from tophat page and I tried this with also the new tophat version 2.1.1 but here is what is happening:

$ ~/bin/tophat-2.1.0.Linux_x86_64/tophat -p 10  -o ./tophat_HCC78  --bowtie1 --fusion-search --keep-fasta-order --no-coverage-search /References_data/References_genome/Homo_sapiens/hg19_tophatfusion_combined/hg19 ../../../fastq/HCC78_trimmed.fastq


[2017-12-13 15:30:36] Beginning TopHat run (v2.1.0)
-----------------------------------------------
[2017-12-13 15:30:36] Checking for Bowtie
                 Bowtie version:        1.2.1.1
[2017-12-13 15:30:36] Checking for Bowtie index files (genome)..
        Found both Bowtie1 and Bowtie2 indexes.
[2017-12-13 15:30:36] Checking for reference FASTA file
Warning: Could not find FASTA file /References_data/References_genome/Homo_sapiens/hg19_tophatfusion_combined/hg19.fa  
[2017-12-13 15:30:36] Reconstituting reference FASTA file from Bowtie index
Executing: /home/iarc/bin/bowtie-1.2.2-linux-x86_64/bowtie-inspect /References_data/References_genome/Homo_sapiens/hg19_tophatfusion_combined/hg19 > ./tophat_HCC78/tmp/hg19.fa
[2017-12-13 15:33:23] Generating SAM header for /References_data/References_genome/Homo_sapiens/hg19_tophatfusion_combined/hg19
[2017-12-13 15:33:26] Preparing reads
     left reads: min. length=20, max. length=371, 21300989 kept reads (196 discarded)
[2017-12-13 15:41:28] Mapping left_kept_reads to genome hg19 with Bowtie 
    [FAILED]
Error running bowtie:
Error while flushing and closing output
terminate called after throwing an instance of 'int'

Does anyone can help me??

[lshepard]

Not an answer, but an advice that you should use the newer aligners (e.g.: STAR, HISAT2).

[Gabriel Wajnberg]

So I have already used STAR-fusion and it worked... but I wanted to test it with tophat-fusion

[lshepard]

Stick it to STAR then. No reason to go back to an older algorithm.

[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. (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, or pseudo-alignment using salmon.

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