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It would be great if there was an option to let Salmon automatically infer the library type instead of taking this from the input file.
E.g. --libType A
This is already inferred by RSeQC infer_experiment.py and the user can re-run the pipeline with the correct strandedness if it was incorrect, however, allowing Salmon to infer it will save this extra step when the user does not know the strandedness.
The text was updated successfully, but these errors were encountered:
Hi @kathleencheung! Apologies for the late response. This seems like a decent proposition as is described here. We could possibly add a parameter to the pipeline such as --salmon_quant_libtype that allows users to override the default behaviour of the pipeline.
I am a bit hesitant to make --libType A the default because getting the strandedness correct will affect the results generated by other QC-based tools used in the pipeline too and this sort of thing can be easily overlooked and the wrong inferences will be made without re-running the pipeline with the correct strandedness e.g. qualimap, stringtie and featurecounts
FIxed in #659 - using --salmon_quant_libtype A will now be able to give you this behaviour and in fact the ability to override any valid --libType setting. Just beware that some of the downstream QC metrics from other tools may not be entirely accurate if there is a discrepancy in the strandedness provided in the samplesheet compared to that auto-inferred by salmon quant.
It would be great if there was an option to let Salmon automatically infer the library type instead of taking this from the input file.
E.g.
--libType A
This is already inferred by RSeQC infer_experiment.py and the user can re-run the pipeline with the correct strandedness if it was incorrect, however, allowing Salmon to infer it will save this extra step when the user does not know the strandedness.
The text was updated successfully, but these errors were encountered: