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where to find hg38 CDS without UTRs

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
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updated by GenoMax GenoMax • written by ta_awwad ta_awwad

2 answers

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

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written by GenoMax GenoMax
  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.
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written by cpad0112 cpad0112

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

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written by ATpoint ATpoint

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