Add Warning for poly(A) libraries

[ojziff]

Description of feature

Hi there,

Many RNAseq accessions do not make explicit whether the RNA prep was total or polyA. I think TrimGalore and cutadapt require -a "A{10}" to trim poly-A tails. My concern is the implications on expression and splicing analyses of not removing polyA tails in oligo(dt) selected libraries?

Like RSeQC infer_experiment.py is used to generate a warning for strandedness fail, I wondered if a similar warning could be created with Qualimap:Genomic Origin or RSeqQC read distribution when intronic reads are < 10% indicative of polyA selection? And suggest to re-run the pipeline with -a "A{10}" ?

Many thanks,
Oliver

[drpatelh]

Hi @ojziff would there be any harm in always trimming poly(A) tails? Just added fastp support in #970 where you can use --trimmer fastp --extra_fastp_args '--trim_poly_x' which should trim the polyA tails by default along with any adapter sequences.

[ojziff]

Thanks @drpatelh. I can't envisage any harm from trimming polyA tails together with the adapter as default.

[drpatelh]

Sweet! Will close this then!