search

jsh58 / Genrich

Detecting sites of genomic enrichment
MIT License
185 stars 27 forks source link

ATAC-seq mode shifted the reads +4 bp for the +strand and -5 bp for the -strand #22

Closed ShuangHe33 closed 5 years ago

ShuangHe33 commented 5 years ago

Thank you for your great tool. In the original paper for ATAC-seq, the authors shifted the reads +4 bp for the +strand and -5 bp for the -strand: http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2688.html I just wonder that if the Genrich considered the Tn5 shifting internally in the -j mode. Thank you in advance!

jsh58 commented 5 years ago

Yes, this was included in the most recent commit, 1 week ago. The shifting is actually +5/-5 to maintain symmetric intervals. I'll be making a new release soon.

ShuangHe33 commented 5 years ago

Yes, this was included in the most recent commit, 1 week ago. The shifting is actually +5/-5 to maintain symmetric intervals. I'll be making a new release soon.

Thanks, I'll look forward for the new release!

jsh58 commented 5 years ago

Here is the new release: Version 0.6