MapSplice Error: could not execute Bowtie

Question

[Nicole]

Hi all,

I'm trying to use MapSplice to analysis my RNA-seq data by the following command

$ python MapSplice_1.15.2/bin/mapsplice_segments.py -Q fq -o outdir -c hg19 -u input.fq -B bowtieIndex
[Tue Jun 27 18:56:19 2017] Checking for chromosomes files or directory
[Tue Jun 27 18:56:19 2017] Checking for chromosomes files or directory passed
[Tue Jun 27 18:56:19 2017] Checking for Bowtie index files
[Tue Jun 27 18:56:19 2017] check reads format
[Tue Jun 27 18:56:20 2017] merge paired end reads remove short
[Tue Jun 27 18:56:28 2017] Mapping reads against hg19 with Bowtie
              [FAILED]
Error: could not execute Bowtie

I indeed have bowtie added in my path. If i type 'bowtie' on terminal, it displaiy the help message. Does anyone meet the same problem?

Answer 1

[Istvan Albert]

The tool will try to execute the bowtie program in the bin directory relative to the script and not based on the system path.

Make sure you have bowtie installed there. The default installation should do that.

[Nicole]

Hi, thank you for your answer. I checked the bin dir under MapSplice, bowtie is located in the same path with the script. May there be any other causes of this error?

Answer 2

[Nicole]

I found the solution. That because the bowtie included in MapSplice didn't support. I download the lastest version of bowtie and copy all the files under bowrie to the bin dir. Then it works. I can't explain why, but it works. I post my solution in case someone might meet the same problem.

Answer 3

[staypositive]

try use mapsplice 2.0 version