TSS coordinates from Ensembl Biomart
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 -
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Annotating TSS: By Transcript or by Gene? Code Validation Help Needed!
written by Rafael Soler •
-
annotationPeaks.pl algorithm for defining promoter-Tss
written by yahelsal •
-
Confused about TSS coordinates
written by srhic •
-
Create snakefile based on R script
written by r.tor •
-
coordinate of BAM and BED
written by yuabrahamliu •
-
bed format, START always bigger than END, no matter which strand?
written by bxia
-
Mapping WGBS probes to CGs (TCGA bed files)
written by sands3 •
-
Official Bed Vs Gff Coordinate Conventions?
written by user
-
Bed Coordinates For Negative/Reverse Strand
written by brianrepko •
-
Where Is The Tss Of A Gene Located In A Bed File?
written by KCC
yes
Move to an answer? Seems like an answer to me.... : )