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t-neumann / slamdunk

Streamlining SLAM-seq analysis with ultra-high sensitivity
GNU Affero General Public License v3.0
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default 12bp trimming from 5' end #94

Closed snaqvi1990 closed 3 years ago

snaqvi1990 commented 3 years ago

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

t-neumann commented 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

snaqvi1990 commented 3 years ago

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

t-neumann commented 3 years ago

Hi Sahin,

no that's fine - leave it at the untrimmed read length.

Best,

Tobi