Drop-seq pipeline

Question

[fluentin44]

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

[ATpoint]

Which obvious reasons?

[fluentin44]

Edited. They typically align to transcriptome as reference (as far as I understand), which means alignment would only occur against mature mRNAs.

[ATpoint]

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.

[fluentin44]

Oooo ok very informative, thankyou very much., ill have a look into it.