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TSS file for hg19

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.

hg19 tss
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updated by ATpoint ATpoint • written by kanwarjag kanwarjag

4 answers

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.

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updated by Ram Ram • written by Chirag Nepal Chirag Nepal

Here you go

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

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updated by Ram Ram • written by Narendra Kumar • Narendra Kumar

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.

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written by ATpoint ATpoint

How to get human refGene hg38 TSS?

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written by Obex33 • Obex33

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.

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written by ATpoint ATpoint

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

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written by Radhu • Radhu

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

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written by ATpoint ATpoint

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

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written by Yan Li • Yan Li

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