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sheffield-bioinformatics-core / periscope

A tool to quantify sub-genomic RNA (sgRNA) expression in SARS-CoV-2 artic network amplicon nanopore sequencing data.
GNU General Public License v3.0
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gRNA counts for illumina data #46

Open cohenp05 opened 2 years ago

cohenp05 commented 2 years ago

Hello,

I'm trying to understand the output for gRNA counts for periscope data applied to illumina sequenced libraries. I see gRNA counts for every ORF in my results and the counts are different per ORF. If I want to know the total gRNA counts for an illumina library (not just the gRNA reads aligning to a given ORF), do I just sum the individual gRNA counts per ORF? Thanks for your help!

Phil C

kjshan commented 1 year ago

I dont have any error when I run this command below "conda env create -f environment.yml conda activate periscope pip install ."

However, when I run periscope, it say "ModuleNotFoundError: No module named 'artic'" and I try install artic package by "conda install -c bioconda artic".

It reported this below: "Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:

Your installed version is: 2.17"

Could you be friendly to help me?