Question: Issue with alignement using Tophat2/Bowtie2 on MiRNA deep sequencing
gravatar for cyrille.laurent.sage
5.0 years ago by
United States
cyrille.laurent.sage0 wrote:


I am trying to use Tophat2/Bowtie2 to align MiRNA from NGS to whole mouse genome. I am using tophat 2.1 and bowtie 2.1 . My command line is

bsub -q priority -W 240:00 -n 8 tophat2 -G /Path/Reference-genes/genes.gtf  -p 8 -N 7 --read-edit-dist 7 --library-type fr-unstranded -o /Path/151013\ LIB18009\ seq/MiRNA-Ampli-test-101315D_output  /Path/NGS_fq/Reference-genes/genome /Path/151013\ LIB18009\ seq/MiRNA-Ampli-test-101315.fq

I am using a local server to run the job, but I got this answer back.


[2015-10-15 09:32:10] Checking for Bowtie

                                  Bowtie version:    

[2015-10-15 09:32:10] Checking for Bowtie index files (genome)..

[2015-10-15 09:32:10] Checking for reference FASTA file

[2015-10-15 09:32:10] Generating SAM header for /groups/corey/Cyrille/NGS_fq/Reference-genes/genome

[2015-10-15 09:32:12] Reading known junctions from GTF file

[2015-10-15 09:32:16] Preparing reads

                 left reads: min. length=20, max. length=25, 920982 kept reads (46944 discarded)

[2015-10-15 09:32:25] Building transcriptome data files /groups/corey/Cyrille/151013 LIB18009 seq/MiRNA-Ampli-test-101315D_output/tmp/genes

[2015-10-15 09:32:38] Building Bowtie index from genes.fa

[2015-10-15 09:39:01] Mapping left_kept_reads to transcriptome genes with Bowtie2


Error running bowtie:

Warning: Output file 'seq/MiRNA-Ampli-test-101315D_output/tmp/genes' was specified without -S.  This will not work in future Bowtie 2 versions.  Please use -S instead.

Extra parameter(s) specified: "-"

Error: Encountered internal Bowtie 2 exception (#1)

Command: /opt/bowtie2-2.1.0/bowtie2-align --wrapper basic-0 -k 60 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-44,0 -p 8 --sam-no-hd -x /Path/151013 LIB18009 seq/MiRNA-Ampli-test-101315D_output/tmp/genes - bowtie2-align exited with value 1

The issue is I do not know where to put -S option. If I put it at the beginning of the command line I got an error -S is not a Tophat2 option. If I tried the --b2-S it is not working. I am kind of stuck here



alignment • 1.9k views
ADD COMMENTlink modified 5.0 years ago by RamRS30k • written 5.0 years ago by cyrille.laurent.sage0
gravatar for RamRS
5.0 years ago by
Baylor College of Medicine, Houston, TX
RamRS30k wrote:

I'd suggest removing the blank spaces in directory names, or using quotes around the directory name. Escape characters may be parsed but not passed along downstream by the shell.

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by RamRS30k
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