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YeoLab / gscripts

General Use Scripts and Helper functions
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Changing genome in analyze_miRli.scala #85

Open broughtonjp opened 8 years ago

broughtonjp commented 8 years ago

When specifying the genome in analyze_miRli.scala, I can't seem to change the genome to a custom one of my choosing. I've tried to change the genome in the bash script that uses analyze_miRli.scala to --genome /projects/ps-yeolab/jbrought/genomes/ecoli/star but STAR keeps using /projects/ps-yeolab/genomes/ce10/star as the default genome. How can I run this with a custom genome?

broughtonjp commented 8 years ago

I've attempted to address this issue by adding a new genome to /projects/ps-yeolab/genomes/. Since map_paired_or_single_with_STAR.py looks for a genome using:

/projects/ps-yeolab/genomes/{0}/star.format(genome)

However, I get the following error from STAR when specifying the newly added genome (ecoli_rel606):

EXITING because of FATAL ERROR: could not open genome file none/genomeParameters.txt
SOLUTION: check that the path to genome files, specified in --genomDir is correct and the files are present, and have user read permsissions

This looks like it is being caused by STAR being given the parameter --genomeDir none.

I've attempted to change the script calling analyze_miRli.scala to use --genome ce10 and this allows mapping to ce10 to occur. But I still can't get mapping to ecoli_rel606.

gpratt commented 8 years ago

Thats because I don't have genome information for ecoli. Do you have the star index for it?

Gabriel Pratt Bioinformatics Graduate Student, Yeo Lab University of California San Diego

On Fri, Feb 5, 2016 at 3:13 PM, James Broughton notifications@github.com wrote:

I've attempted to address this issue by adding a new genome to /projects/ps-yeolab/genomes/. Since map_paired_or_single_with_STAR.py looks for a genome using:

/projects/ps-yeolab/genomes/{0}/star.format(genome)

However, I get the following error from STAR when specifying the newly added genome (ecoli_rel606):

EXITING because of FATAL ERROR: could not open genome file none/genomeParameters.txt SOLUTION: check that the path to genome files, specified in --genomDir is correct and the files are present, and have user read permsissions

This looks like it is being caused by STAR being given the parameter --genomeDir none.

I've attempted to change the script calling analyze_miRli.scala to use --genome ce10 and this allows mapping to ce10 to occur. But I still can't get mapping to ecoli_rel606.

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/85#issuecomment-180616739.

broughtonjp commented 8 years ago

/projects/ps-yeolab/genomes/ecoli_rel606/star