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epi2me-labs / wf-transcriptomes

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How to set the 'min_feature_expr' parameter to preserve rare transcripts? #54

Closed WQQIGDB closed 6 months ago

WQQIGDB commented 8 months ago

Ask away!

I want to preserve the low-abundance transcripts in my samples by reseting the min_feature_expr to 1. If so, does that mean I can preserve the transcripts with only one mapped reads? Is it resonable to use such a value? And is it necessary to reset other parameters to fulfil my purpose? I'll appreciate your suggestions! nextflow_schema json

nrhorner commented 8 months ago

Hi @WQQIGDB

min_feature_expr is set to reduce noise and to aid with statistical inference during differential expression. I wouldn't recommend setting this value to 1, but I believe it should 'work' although I have not tried it.

sarahjeeeze commented 6 months ago

Hi, closing this through lack of response, open another issue if you have any more questions.