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How to get human cDNA sequences together with UTR regions?

Dear all,

I have downloaded the human genome and gtf files from Gencode. Based on these two files I want to generate a fasta file that has cDNA sequences including 5' and 3' UTRs for protein-coding genes only. What is the simplest and fastest way to do this?

Would this script work? gffread -w transcripts.fa -g genome.fa transcripts.gtf

Thank you.

transcripts cdna genome rna-seq
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updated by Istvan Albert Istvan Albert • written by Apex92 • Apex92

cDNA is the "complementary" DNA to the mRNA transcript. mRNA transcripts include UTRs, so the cDNA sequence should too.

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written by i.sudbery i.sudbery

2 answers

The command you specify will concatenate the exon sequence for each transcript and as long as the exons contain the UTRs you will get those.

To keep only protein-coding exons, you might need to preprocess the GTF file to keep only those that have gene_type "protein_coding" tag.

In general, though I would recommend downloading the CDNA files from the same source and filtering that with some other method.

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written by Istvan Albert Istvan Albert

This probably wants to be transcript_biotype, not gene_biotype as its possible to have non-coding transcripts of coding genes.

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written by i.sudbery i.sudbery

Thank you for your comments. At the end of the day, I tried this approach so this might be helpful for others as well. And I would also be happy to get your feedback in case I encountered any mistakes.

  1. I downloaded both genome and gtf files from Gencode.

  2. Preprocessed the gtf file and converted it to a bed format in the structure below (keeping only protein-coding transcripts): chr start end transcript_name type strand.

  3. Used bedtools to extract sequences in fasta format from the genome file using bedtools as
    bedtools getfasta -fi genome.fa -bed gencode_protein_coding.bed -name > hsa_protein_coding_transcripts.fa

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written by Apex92 • Apex92

as far as I know the bedtools getfasta can only concatenate exons if you had it in the 12 column format with block information,

if all you had was the 6 column BED as you describe it, then how could it identify the exons that form a transcript?

I believe the method that you describe will generate the unspliced transcript

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written by Istvan Albert Istvan Albert

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