bed file for hg38 transcripts

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7.1 years ago

rbpdee ▴ 50

Hi folks,

I am looking for the genomic coordinates of the cDNA sequences (exons) given in the file located at "ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz". A bed file would do.

Where can I find this bed file?

Thanks!

RNA-Seq alignment • 3.5k views

ADD COMMENT • link 7.1 years ago by rbpdee ▴ 50

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Have you tried BioMart at Ensembl site?

ADD REPLY • link 7.1 years ago by GenoMax 141k

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BioMart has a lot of options, but I do not know the right ones. So, I have been avoiding BioMart. If you know the options, let me know.

I am planning to collect the exonic coordinates from the associated GTF file.

ADD REPLY • link 7.1 years ago by rbpdee ▴ 50

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Take a look at this video tutorial from Ensembl. Give BioMart a whirl and ask if any questions come up.

ADD REPLY • link 7.1 years ago by GenoMax 141k

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Thanks, I will go through the tutorial.

ADD REPLY • link 7.1 years ago by rbpdee ▴ 50

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