Hello,
I am using STAR_2.3.0e.Linux_x86_64 to align only the first 25b of my paired-end reads, with the parameters:
--outFilterMatchNmin 40
--clip5pNbases 4 (there 4 random pairs before the PCR primer that I want to remove)
--clip3pNbases 71 (in order to only keep the first 25 bases)
--outSAMattributes All
--outFilterMultimapNmax 3
--outFilterMismatchNmax 5
--outFilterMismatchNoverLmax 0.05
--alignIntronMax 1
--alignMatesGapMax 740
I have cases like below where one mate of a pair is multiply mapped but with alignments containing a sum of matches that is less than 40, although I asked for a minimum of 40 matches using the parameter --outFilterMatchNmin.
I don't understand why these alignments are recorded while they have less than 40 perfect matches (required using --outFilterMatchNmin).
Any advice or guidance will be welcomed, thank you!
Best,
Anne
HISEQ:97:H8U2HADXX:1:1101:3459:2064 355 CXCL3 328 3 4S25M71S = 428 111 AATTATGACAGGGTGGGGAACTGGAGGGTGGGGGGATTGAAATGCAAGCAATTAGTGGATCACTGTTAGGGTAAGGGAATGTATGTACACATCTATTTTT @C@DDFFFHHGGFACHEGIGGIGIHIII?DHIJJD8BDCDDCDDDDCCDDDDDCCDDDCDABDDDDDDDDD9ACCDDBDDDCCCD>B>CCCCDCDEEEED NH:i:2 HI:i:2 AS:i:34 nM:i:0 jM:B:c,-1 jI:B:i,-1
HISEQ:97:H8U2HADXX:1:1101:3459:2064 403 CXCL3 428 3 81S11M8S = 328 -111 TTTGCTTTATAGGTTATTTTATTTTTATTTCTCTAATTCCTGGGTTTTTTTTTTTCTCTTAAAAAAAATATTTTTTATTTTCTTTTTTTTTATTGCCTTT #################################################################################################### NH:i:2 HI:i:2 AS:i:34 nM:i:0 jM:B:c,-1 jI:B:i,-1
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