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STAR mapping parameter

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

Thanks

rna-seq
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updated by sklages sklages • written by mxlsherry1992 • mxlsherry1992

i think outFilterMatchNmin is the parameter you are looking for

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written by hafiz.talhamalik hafiz.talhamalik

1 answer

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
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written by sklages sklages

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