My goal is to match a custom single cell type library with unknown barcode locations across reads but known sequences: I have made a 'genome' of ~70nt of each 'read' (17mX70nt contigs) and have aligned putative barcodes (~70kX32nt) against this. I specifically want the 32nt barcodes and 70nt reads to be locally aligned very similar to a standard Smith-Waterman alignment and mismatches on either end of the 32nt be penalized and not soft-clipped. Naturally the reads (barcodes here) need to be mapped to 100s or 1000s locations and soft-clipping is not desired here. These are my STAR options:
STAR \
--runThreadN 16 \
--outFileNamePrefix my_run \
--alignEndsType EndToEnd \
--outSAMmode NoQS \
--scoreDelOpen 0 \
--scoreDelBase -1 \
--scoreInsOpen 0 \
--scoreInsBase -1 \
--outFilterMultimapNmax 10000 \
--winAnchorMultimapNmax 10000 \
--seedPerReadNmax 10000 \
--seedPerWindowNmax 10000 \
--outSAMattributes NH HI AS nM NM MD \
--outFilterMismatchNmax 2 \
--genomeDir ./my_ref/ \
--readFilesIn my.fasta
This setting works relatively well however I would like to ask if there is there a set of aligner parameters to allow me to swap my reference and reads in order to have a more convectional mapping?
