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Just taking some notes here
I found strong batch effect in polyA. I am thinking of the following plan:
- salmon parameters:
--seqBias--gcBias--posBias. The documentation also suggest checking GC bias from multiQC distributions https://salmon.readthedocs.io/en/latest/salmon.html - combat salmon quant.sf prior to running the next step of labrat.
Originally posted by @algaebrown in #4 (comment)
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