Question: TSS coordinates from Ensembl Biomart
2
gravatar for ZheFrench
4 months ago by
ZheFrench130
France
ZheFrench130 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 • 227 views
ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 4 months ago by ZheFrench130
1

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

yes

ADD REPLYlink written 4 months ago by Pierre Lindenbaum108k

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

ADD REPLYlink written 4 months ago by Sean Davis24k
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