STAR set --sjdbOverhang value
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.
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youyi •
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linjc.xmu •
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linjc.xmu •
1 answer
You know the manual says about sjdbOverhang
In most cases, a generic value of 100 will work as well as the ideal value.
http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STAR.posix/doc/STARmanual.pdf
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Why don't you use sjdbOverhang 101 for your 150bp paired-end data?
I used --sjdbOverhang 149. How did you?