Question

Fraction count for multi mapping reads; how to generate input file for Deseq2 for this fraction count

0

Entering edit mode

tg369 ▴ 10

@tg369-9320

Last seen 4.7 years ago

United Kingdom

Hi,

I was doing repeat analysis from RNA seq data and learn that featureCounts() function ("Rsubread" package) can provide fraction counts for multi-mapping reads. However, DEseq2 doesn't take fraction counts as an input. If I need to use deseq2 for differential expression analysis, what do you suggest?

Rounding up those fraction counts might not be ideal.

Thank you in advance for your advice and am looking forward to that.

deseq2 • 2.0k views

ADD COMMENT • link updated 9.0 years ago by Michael Love 43k • written 9.0 years ago by tg369 ▴ 10

score 0 · Answer 1 · 2015-12-11

0

Entering edit mode

Michael Love 43k

@mikelove

Last seen 2 days ago

United States

Rounding the fractional counts is my recommendation. This is well within the expected sampling variation of a technical replicate.