Closed snaqvi1990 closed 3 years ago
Hi Sahin,
this is more a Quantseq specific setting where the kit manufacturer recommends to trim the first 12bp from the 5' end.
Best,
Tobi
Hi Tobi,
Thanks for the response. If the trimming is done, should the -l parameter in slamdunk count then be adjusted to accounted for this (i.e. if sequenced read length is 150, -l should be 138)?
Thanks, Sahin
Hi Sahin,
no that's fine - leave it at the untrimmed read length.
Best,
Tobi
Hello,
Another unrelated question - slamdunk by default seems to trim 12bp from the 5' end of the read - what is the purpose of this step? Is it related to read quality, or something more specific to SLAMseq analyses?
Thanks, Sahin