Question

STAR mapping parameter

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4.5 years ago

mxlsherry1992 ▴ 80

Hi, if you know what parameter in STAR can restrict the minimum bases matched to the genome..?

Thanks

RNA-Seq • 1.7k views

ADD COMMENT • link updated 4.5 years ago by sklages ▴ 170 • written 4.5 years ago by mxlsherry1992 ▴ 80

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i think outFilterMatchNmin is the parameter you are looking for

ADD REPLY • link 4.5 years ago by hafiz.talhamalik ▴ 350

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What was not clear after reading the documentation?

ADD REPLY • link 4.5 years ago by WouterDeCoster 47k

score 0 · Answer 1 · 2019-10-24

this is sth. you can start with. We used these for testing with smal RNA mapping:

outFilterMatchNmin           = alignment will be output only if the number of matched bases is higher than or equal to this value.
outFilterMatchNminOverLread  = sam as outFilterMatchNmin, but normalized to the read length
outFilterScoreMinOverLread   = same as outFilterScoreMin, but  normalized to read length