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where can i find ENSG_coord.txt or similiar plain file in different build? #428

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yc-long opened this issue Apr 1, 2024 · 1 comment

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@yc-long
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yc-long commented Apr 1, 2024

in the .py scritpt, it was annoted as
"default='ENSG_coord.txt', help='a file with columns GENE, CHR, START, and END, where START and END are base pair coordinates of TSS and TES. This file can contain more genes than are in the gene set. We provide ENSG_coord.txt as a default.')"
but i cannot find this file anywhere.
thank you in advance

@aksarkar
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aksarkar commented May 5, 2024

@yc-long You can generate a compatible file using the GENCODE GTF https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_45/gencode.v45.annotation.gtf.gz

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