Using rmats on bioconda

Question

[gcottone]

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

[Prakash]

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

[gcottone]

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

Answer 1

[WouterDeCoster]

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

Answer 2

[Arup Ghosh]

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