marbl/CHM13

refSS regions of CHM13v2 ?

unique379r opened this issue · 2 comments

unique379r commented

Hi
I am looking for TSS region similar to hg38 (http://reftss.clst.riken.jp/reftss/Main_Page) that can be utilized by SQANT3_QC. Please direct me if you have any annotation.

Thanks
Rupesh

arangrhie commented

Hi Rupesh,

Did you find what you need? I am not sure which TSS you need. Could you use one of the annotations available here?

mechealeth commented

Hi Rupesh,

Did you find what you need? I am not sure which TSS you need. Could you use one of the annotations available here?

Hi, I also have the same problem. I used human.refTSS_v3.1.hg38.bed file from https://reftss.riken.jp/datafiles/3.1/human/ and liftover it to hs1 using https://genome.ucsc.edu/cgi-bin/hgLiftOver , but there are around 200 sites fail to liftover. I wonder if there any refTSS for CHM13v2 assemble and I would like use it for SQANT3_QC input.
thanks
min