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maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
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3primeseq question #894

Closed sunta3iouxos closed 1 year ago

sunta3iouxos commented 1 year ago

Dear all, where is that module applicable? I am asking because there are various 3'prime RNA-seq protocols there (quant-seq, NEBNext Single Cell/Low Input RNA , the illumina 3'-Seq, Ovation SoLo). Each one of those site on their site specific trimming and mapping details. Would it be possible to provide an overview of the method and for which RNA/library preperation applies?

Thank you

katsikora commented 1 year ago

Hi sunta3iouxos,

the 3'prime RNA-seq mode has been tested with the Lexogen 3'Seq/ Illumina. We may be able to test it with other prep kits in the future and adjust as applicable. Trimming and mapping parameters can be controlled with --trimmerOptions and -alignerOptions in any case.

Best wishes,

Katarzyna