Question

ProkSeq

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2.3 years ago

sgadila • 0

Hello everyone, I was wondering if anyone has used ProkSeq pipeline for bacterial RNA-seq analysis? If so, could you please help me download and setup the analysis pipeline for MacOS? Thanks

data Prokseq analysis Bacterial RNA-seq • 1.1k views

ADD COMMENT • link updated 2.1 years ago by plwalker.micro • 0 • written 2.3 years ago by sgadila • 0

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Were you able to complete a run of the whole ProkSeq pipeline? I have never been able to get past the DEseq2 step.

ADD REPLY • link 2.1 years ago by plwalker.micro • 0

score 0 · Answer 1 · 2022-01-03

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2.3 years ago

GenoMax 141k

If you are referring to this pipeline then your best bet is to use conda for the install. Use first part of this tutorial to install conda: Creating workflows with snakemake and conda then follow the directions linked for ProkSeq.

ADD COMMENT • link 2.3 years ago by GenoMax 141k

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Thank you for your response. I have installed conda on my Mac OS according to the instructions provided in the Biostar handbook. Once I install ProkSeq, would that be compatible with the rest of the environment listed in the handbook?

ADD REPLY • link 2.3 years ago by sgadila • 0

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Not sure how this is related to biostar handbook but if you are working with different conda environments then there should be no issues.

ADD REPLY • link 2.3 years ago by GenoMax 141k