alevin on 5'-tagged scRNAseq

[carneiro-m]

Hi,
I was wondering if alevin could be used on 5'-tagged scRNAseq (10x chemistry) gene expression and V(D)J libraries.

Thanks

[k3yavi]

Hi @carneiro-m ,
Yes, you just have to change the library type to -lISF from -lISR.
One caveat though, unfortunately, even if the data has read sequence on both its end, alevin will use only one end for mapping.

[carneiro-m]

Hi @carneiro-m ,
Yes, you just have to change the library type to -lISF from -lISR.
One caveat though, unfortunately, even if the data has read sequence on both its end, alevin will use only one end for mapping.

Hi @k3yavi, thank you so much.

[rfarouni]

So which --chemistry flag in Cell Ranger does the change to -lISF correspond to? Is it SC5P-R2 or fiveprime? https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count

Also since salmon/alevin can detect the library type automatically, would detect the correct library in the case of 5'-tagged scRNAseq 10X Feature barcode?