Question

STAR index generation option --sjdbOverhang for paired-end ?

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7.9 years ago

XBria ▴ 90

Hi,

To generate indices for paired-end samples for example with 75 forward and 75 reverse shall I write 75-1 in the option --sjdbOverhang or 150-1 ?

RNA-Seq • 4.3k views

ADD COMMENT • link updated 7.9 years ago by Hussain Ather ▴ 990 • written 7.9 years ago by XBria ▴ 90

score 0 · Answer 1 · 2017-11-30

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7.9 years ago

Hussain Ather ▴ 990

74.

The answer is explained here.

ADD COMMENT • link 7.9 years ago by Hussain Ather ▴ 990

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Yes, that's correct. It's just read length - 1.

ADD REPLY • link 7.9 years ago by mforde84 ★ 1.4k