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alexdobin / STAR

RNA-seq aligner
MIT License
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STAR after alignment I get too many short Cigar matched fragments #1980

Open lxy04 opened 1 year ago

lxy04 commented 1 year ago

when I see the bam in IGV, I found that too many too sharp peaks, and they are such as ' cigar=20S13M117S', What can I do to filter these peaks? Is outFilterMatchNmin or seedSearchStartLmax? Sincerely

lxy04 commented 1 year ago

actually, I want to filtered the cigar match < 45

alexdobin commented 1 year ago

What STAR options did you use? They allowed very short alignments.

yagam-fluent commented 11 months ago

Hi Alex,

I'm running into a similar problem as lxy04. What parameters control the minimum alignment length?

Thanks, Yigal

alexdobin commented 11 months ago

Hi Yigal,

this parameters control the minimum allowed alignment length:

outFilterScoreMin               0
    int: alignment will be output only if its score is higher than or equal to this value.

outFilterScoreMinOverLread      0.66
    real: same as outFilterScoreMin, but  normalized to read length (sum of mates' lengths for paired-end reads)

outFilterMatchNmin              0
    int: alignment will be output only if the number of matched bases is higher than or equal to this value.

outFilterMatchNminOverLread     0.66
    real: sam as outFilterMatchNmin, but normalized to the read length (sum of mates' lengths for paired-end reads).
lxy04 commented 11 months ago

Hi Alex, these parameters are useful!

Many thanks! Li