Question: TSS coordinates from Ensembl Biomart
2
gravatar for ZheFrench
11 months ago by
ZheFrench180
France
ZheFrench180 wrote:

When you use biomart you can get 1-based TSS start coordinate. If you want to transform this coordinate to 0-based format you need to remove 1, whatever the strand is , right ?

If strand + , TSS is chr11 48488717 coordinate in biomart. If you want bed format, it will be :

chr11 48488716 48488717 name signalValue +

If strand - , TSS is chr11 64879712 coordinate in biomart. If you want bed format, it will be :

chr11 64879711 64879712 signalValue 0 -

biomart ensembl • 408 views
ADD COMMENTlink modified 10 months ago by Biostar ♦♦ 20 • written 11 months ago by ZheFrench180
1

you need to remove 1, whatever the strand is , right ?

yes

ADD REPLYlink written 11 months ago by Pierre Lindenbaum116k

Move to an answer? Seems like an answer to me.... : )

ADD REPLYlink written 11 months ago by Sean Davis25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1236 users visited in the last hour