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Will the --outfiltermismatchNmax in the STAR works for the single end reads?

Dear all,

I have some single end reads and I would like to do the mapping step with STAR. But depends on the manual of STAR the -- outFilterMismatchNmax is for setting the maximum number of mismatches per pair. So I was wondering if this --outFilterMismatchNmax will also work for the single end reads? And how would it work?

rna-seq alignment
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updated by ATpoint ATpoint • written by codezy • codezy

In case you have varying read lengths , you can also use --outFilterMismatchNoverLmax:

int: alignment will be output only if its ratio of mismatches to mapped length is less than this value

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written by michael.ante michael.ante

1 answer

The manual says int: alignment will be output only if it has no more mismatches than this value., it does not seem to be an explicit paired-end option. In the worst case, take some reads, introduce a couple of mismatches to a read that perfectly matches and then see what happens.

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written by ATpoint ATpoint

@ATpoint Thank you for your answer. I have also read this int, but in page 9 of STAR manual they said "--outFilterMismatchNmax 999 maximum number of mismatches per pair, large number switches off this lter" So I confused about that.

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written by codezy • codezy

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