SC-RNASeq data mappability with STAR
Hello all,
I wonder what is a "good" percentage of uniquely mapped reads for a single cell in STAR. Currently I get around 50% given that there is a relaxation of number of matched bases (--outFilterMatchNminOverLread 0). Without this, I would get around 30% unique matches and a whole pile of unaligned reads (too short).
Thank you,
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