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Question: RIPseeker peak calling parameters for TruSeq Samll RNA stranded library
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gravatar for ofonov
14 months ago by
ofonov10
Norway/Oslo
ofonov10 wrote:

Hi,

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!

 

ADD COMMENTlink written 14 months 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 5 hours ago by samantha.jeschonek0
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