Comments (3)
Hi @drneavin
Ns in the middle of read sequences limit seed searching, so they cause lower alignment rates.
You can try to increase alignment sensitivity by reducing --winAnchorMultimapNmax
from the default 50 to 30,20 or 10 and reducing --seedSearchStartLmax
from the default 50 to 30 or 20.
from star.
Thanks @alexdobin! I'll give those a try.
Also wondering if that will that also help if the Ns are in the barcodes or UMIs? I suspect that will be more challenging?
from star.
Hi @drneavin
these parameters only apply to mapping the cDNA portion of the read. For cell barcodes, STARsolo can match the sequence with one N to the passlist with --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts
option. UMIs with Ns are always discarded.
from star.
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