Drop-seq pipeline
Hi,
Does anyone have experience of modifying the drop-seq pipeline from the McCarroll lab to allow for a certain proportion of multimapping reads? Im aware that tools like Alevin and other pseudo-aligners are pretty adept at dealing with them, however I would like to be able to process snRNA-seq data, which raises issues with using pseudoaligners as they typically align to the transcriptome as a reference.
Thanks, Matt
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Which obvious reasons?
Edited. They typically align to transcriptome as reference (as far as I understand), which means alignment would only occur against mature mRNAs.
It aligns against what you give it. I personally always use the expanded transcriptome (exon+intron) with the entire genome as decoy, see for example here for code suggestions to do exactly that: https://combine-lab.github.io/alevin-tutorial/2020/alevin-velocity/
It is well capable of dealing with snRNA and probably even your best choice.
Oooo ok very informative, thankyou very much., ill have a look into it.