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databio / dnameth_pipelines

PEP-compatible pipelines for DNA methylation data (RRBS, WGBS)
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Tool naming #22

Open vreuter opened 5 years ago

vreuter commented 5 years ago

Why does a script for which the name suggests RNA run here? What's this tool do?

`python /sfs/qumulo/qhome/vpr9v/code/dnameth_pipelines/src/tools/bisulfiteReadFiltering_forRNA.py
nsheff commented 5 years ago

@jklughammer any recollection here?

jklughammer commented 5 years ago

yeah, we created this for the core-seq protocol, which was supposed to assesses DNA methylation and RNA in the same sequencing library. In RNA mode this script was supposed to identify the reads that originated from RNA. I guess it is not really needed in a standard DNA methylation pipeline.

vreuter commented 5 years ago

OK cool, that makes sense.

vreuter commented 5 years ago

This is the filtration step in the WGBS pipeline. @nsheff is it fine to leave this in, or should we switch to a different filtration strategy?

jklughammer commented 5 years ago

Sorry for the confusion: the rna mode is not needed for normal methylation analysis. The history of this script is that it started out as a script solely for the purpose of filtering reads in a DNA methylation setting (specifically for the epignome protocol). When we worked on CORE-seq we adapted this script to basically assign the reads to whether they come from DNA (converted) or RNA (not converted, spliced etc).