TSS file for hg19

Question

[kanwarjag]

I am sure this may have been answered already, Can some one direct me to a bed file of TSS of hg19 or how can be extract / clean it. I googled it but could not find it.

[rohitsatyam102]

This post can guide you: https://randomstate.net/2018-06-28-getting-refseq-gene-tss-from-ucsc/

Answer 1

[Chirag Nepal]

Go to UCSC table browser and select hg19 gene models from either ensembl/Refseq/Gencode, which is either a GTF or BED file.

If gene is on + strand, col-2 is TSS and if gene is on -ve strand, col3 is TSS.

Answer 2

[Narendra Kumar]

Here you go

http://sourceforge.net/projects/seqminer/files/Reference%20coordinate/

Answer 3

[Shicheng Guo]

human refGene hg19 TSS:

https://raw.githubusercontent.com/Shicheng-Guo/AnnotationDatabase/master/hg19/refGene_hg19_TSS.bed

human refGene hg38 TSS:

https://raw.githubusercontent.com/Shicheng-Guo/AnnotationDatabase/master/hg38/refGene.hg38.TSS.bed

[ATpoint]

I strongly recommend against downloading files from non-official repositories. Always download from the official sources like UCSC, GENCODE, etc. You have no control over what the uploader might have done with the file. Not saying it was not proper, it is just not guaranteed.

[Obex33]

How to get human refGene hg38 TSS?

[ATpoint]

Download the GTF from their official repository at NCBI, then filter for entries of the type "transcript" and take the start coordinate for plus-strand features and end coordinate for bottom strand features. That's it.

[Radhu]

Is there any tool for doing this or just a bash script ?

[ATpoint]

It's really just some if/else awk command.

[Shicheng Guo]

Try this one:

https://raw.githubusercontent.com/Shicheng-Guo/AnnotationDatabase/master/hg38/refGene.hg38.TSS.bed

Answer 4

[Yan Li]

For refGene_hg19_TSS.bed file, the TSS site of "-" strnad should subtract 1, because the bed file not contain the last coordinate.