Use of aligners (preferably STAR) for read-barcode matching
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?
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