where to find hg38 CDS without UTRs

Question

[ta_awwad]

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

Answer 1

[GenoMax]

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

Answer 2

[cpad0112]

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

[ATpoint]

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