Hi,
I am new to NGS analysis. I was trying to follow a protocol for an analysis that calls on tophat2 on a cluster. After looking at some previous posts on this forum, I am trying to specify the absolute path. The code I execute is:
% tophat2 -p 8 -o S1_R1_out -G /home/bs/mm10/Genes/genes.gtf /home/bs/mm10/Sequence/Bowtie2Index/genome S1_R1_1.fastq S1_R1_2.fastq
However, I get the following error message:
==========================
[2014-11-10 09:26:35] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2014-11-10 09:26:35] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.
==========================
I checked and bowtie2 is in my path:
% bowtie2
No index, query, or output file specified!
Bowtie 2 version 2.2.3 by Ben Langmead ([email protected], www.cs.jhu.edu/~langmea)
Usage:
bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]
What am I doing wrong?
thanks!
I am new to NGS analysis. I was trying to follow a protocol for an analysis that calls on tophat2 on a cluster. After looking at some previous posts on this forum, I am trying to specify the absolute path. The code I execute is:
% tophat2 -p 8 -o S1_R1_out -G /home/bs/mm10/Genes/genes.gtf /home/bs/mm10/Sequence/Bowtie2Index/genome S1_R1_1.fastq S1_R1_2.fastq
However, I get the following error message:
==========================
[2014-11-10 09:26:35] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2014-11-10 09:26:35] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.
==========================
I checked and bowtie2 is in my path:
% bowtie2
No index, query, or output file specified!
Bowtie 2 version 2.2.3 by Ben Langmead ([email protected], www.cs.jhu.edu/~langmea)
Usage:
bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]
What am I doing wrong?
thanks!
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