Question

STAR set --sjdbOverhang value

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6.3 years ago

linjc.xmu ▴ 30

Dear all, STAR manual said set --sjdbOverhang at readlength-1. I am confused by this with two questions.

If I generated genome index by setting it at 100 previously, and now I have a PE150 reads, should I re-generate genome index by setting it at --sjdbOverhang 149?
If I use --clip3pNbases 50 during mapping, should I set --sjdbOverhang at 99 (is from: 150 -50 -1)?

Thanks for your help. Best.

rna-seq • 4.6k views

ADD COMMENT • link updated 4.2 years ago by youyi • 0 • written 6.3 years ago by linjc.xmu ▴ 30

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Why don't you use sjdbOverhang 101 for your 150bp paired-end data?

ADD REPLY • link 6.3 years ago by k.kathirvel93 ▴ 310

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I used --sjdbOverhang 149. How did you?

ADD REPLY • link 4.2 years ago by youyi • 0

score 2 · Accepted Answer · 2018-09-12

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6.3 years ago

swbarnes2 14k

You know the manual says about sjdbOverhang

In most cases, a generic value of 100 will work as well as the ideal value.

ADD COMMENT • link 6.3 years ago by swbarnes2 14k