sc/sn RNASeq
Hi Everyone
I am using cellranger to align my sc/snRNAaseq reads. I use --force cells --include introns , I get this error:
*High Fraction of Reads Mapped Antisense to Genes 38.9% Ideal < 10%. This can indicate use of an unsupported chemistry type (e.g. using Single Cell V(D)J for gene counting). Application performance is likely to be affected.*
If I remove the include introns options, I don't get the error. But I need to incldue introns as I am doing sc/snRNASeq. Any hint how to fix this? Thanks
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Which chemistry did you use ?
its 10x. I don't know more, is there a way to tell? The data is passed to me. I used --chromium as option? The chemistry detected automatically by cellranger says Single Cell 3' v3
Contact the person/platform who performed the lib prep + sequencing to be sure which chemistry you used. Also be sure to knowif you work on single cells or on single nucleis.
Ok, thanks. How would it be different if it is single nucleis? Just include introns? Thanks