Using rmats on bioconda

Question: Using rmats on bioconda

19 months ago by

gcottone • 0 wrote:

Hi I am new to using both rmats as well as the bioconda system. I am curious as to if I put the same input into the line in conda as I would on rmats, i.e.;

"python RNASeq-MATS.py -b1 testData/231ESRP.25K.rep-1.bam,testData/231ESRP.25K.rep-2.bam -b2 testData/231EV.25K.rep-1.bam,testData/231EV.25K.rep-2.bam -gtf gtf/Homo_sapiens.Ensembl.GRCh37.72.gtf -o bam_test -t paired -len 50 -c 0.0001 -analysis U -libType fr-firststrand"

What should I change to start getting output?

thanks

rna-seq • 1.0k views

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modified 19 months ago by Arup Ghosh ♦ 2.8k • written 19 months ago by gcottone • 0

I think your question is not directly related to bioinformatics. However, I would try which python . If python is available from your bioconda --> ~/anaconda3/bin/python, then command will run otherwise no. Then you may need to do conda activate

ADD REPLY • link written 19 months ago by Prakash • 2.1k

Ok, I am just curious if you have any recommendations to other forums that may be able to help more? Since this isn't directly related to bioinformatics

ADD REPLY • link written 19 months ago by gcottone • 0

19 months ago by

WouterDeCoster ♦ 45k

Belgium

WouterDeCoster ♦ 45k wrote:

Conda is just the package manager, it doesn't really* change how you execute the software.

*to be technically correct: for e.g. Java tools a wrapper script is used, so the name of the executable can be different

ADD COMMENT • link written 19 months ago by WouterDeCoster ♦ 45k

19 months ago by

Arup Ghosh ♦ 2.8k

India

Arup Ghosh ♦ 2.8k wrote:

Assuming that you have installed rmats 4.0.2 using the bioconda channel and using Anaconda2 (as the tool requires python 2.7) the RNASeq-MATS.py script will be available in ~/anaconda2/bin/. Also, the tool is looking for text inputs in -b1 and -b2 as per the tool documentation, not sure if the command-line input will work. So a working command-line will look like the following example.

~/anaconda2/bin/python ~/anaconda2/bin/RNASeq-MATS.py --b1 b1.txt --b2 b2.txt --gtf gtfFile --od outDir -t readType --nthread nthread --readLength readLength

ADD COMMENT • link modified 19 months ago • written 19 months ago by Arup Ghosh ♦ 2.8k

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