Question: bed file for hg38 transcripts
1
gravatar for rbpdee
2.1 years ago by
rbpdee20
United States
rbpdee20 wrote:

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 • 1.1k views
ADD COMMENTlink written 2.1 years ago by rbpdee20

Have you tried BioMart at Ensembl site?

ADD REPLYlink written 2.1 years ago by genomax65k

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 REPLYlink written 2.1 years ago by rbpdee20
1

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

ADD REPLYlink written 2.1 years ago by genomax65k

Thanks, I will go through the tutorial.

ADD REPLYlink written 2.1 years ago by rbpdee20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 884 users visited in the last hour