Question

where to find hg38 CDS without UTRs

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6.3 years ago

ta_awwad ▴ 350

Hello everyone, I am looking for Human protein-coding transcript sequences WITHOUT UTRs in fasta format if possible.. any Idea where to find such file?

Best, TA

RNA-Seq genome assembly alignment • 1.3k views

ADD COMMENT • link updated 6.3 years ago by GenoMax 147k • written 6.3 years ago by ta_awwad ▴ 350

score 1 · Answer 1 · 2018-07-31

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6.3 years ago

GenoMax 147k

You should be able to get them from BioMart at Ensembl. Video tutorial available for BioMart.

ADD COMMENT • link 6.3 years ago by GenoMax 147k

score 1 · Answer 2 · 2018-07-31

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6.3 years ago

cpad0112 21k

Get gtf with all annotations (for all coding genes)
Chuck 3' and 5' UTRs out from gtf
use tools such as getFasta to get protein coding transcript sequences.

ADD COMMENT • link 6.3 years ago by cpad0112 21k

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Simply greping or awking for 'CDS' as the feature in the GTF, followed by bedtools getfasta on the resulting coordinates does the job.

ADD REPLY • link 6.3 years ago by ATpoint 85k