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ProkSeq

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
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updated by plwalker.micro • plwalker.micro • written by sgadila • sgadila

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

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written by plwalker.micro • plwalker.micro

1 answer

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.

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written by GenoMax GenoMax

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?

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written by sgadila • sgadila

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

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written by GenoMax GenoMax

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