Question: RIPseeker peak calling parameters for TruSeq Samll RNA stranded library
gravatar for ofonov
2.7 years ago by
ofonov10 wrote:


I got somewhat lost in the parameters of RIPseeker. I would like to do peak calling on the data produced with TruSeq Smalll RNA Illumina protocol. It is a stranded library prep protocol -  sequencing reads from read 1 map to the antisense strand and those from read 2 map to the sense strand.

Should I use

reverseComplement = TRUE or FALSE

strandType = "+", "-", or "*"


Thank you!


ripseeker rna-seq rip • 508 views
ADD COMMENTlink written 2.7 years ago by ofonov10

Did you ever arrive at a solution? 

Would also love an answer to this.  The Truseq prep protocol uses --fr-stranded technology (if that helps).

ADD REPLYlink written 18 months ago by samantha.jeschonek0
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