Question: TOPHAT error in mapping left_kept_reads step during a mapping with fusion search with bowtie1
gravatar for Gabriel Wajnberg
15 months ago by
Gabriel Wajnberg60 wrote:

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:
[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 
Error running bowtie:
Error while flushing and closing output
terminate called after throwing an instance of 'int'

Does anyone can help me??

bowtie tophat fusion • 984 views
ADD COMMENTlink written 15 months ago by Gabriel Wajnberg60

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

ADD REPLYlink written 15 months ago by lshepard210

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

ADD REPLYlink written 15 months ago by Gabriel Wajnberg60

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

ADD REPLYlink written 15 months ago by lshepard210

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.

ADD REPLYlink modified 15 months ago • written 15 months ago by WouterDeCoster37k
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