Bulk Download all CDS and UTRs of known genes from ENSEMBL

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5.5 years ago

Aishwarya Kulkarni ▴ 90

I want to download all the CDS and UTR coordinates (based on gene id ) from ensembl, is there a way to do that through biomart or biomaRt package?

UTR CDS ensembl • 1.6k views

ADD COMMENT • link updated 5.5 years ago by ATpoint 85k • written 5.5 years ago by Aishwarya Kulkarni ▴ 90

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Can't you parse that info from the gtf?

ADD REPLY • link 5.5 years ago by swbarnes2 14k

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Yes I just realized that after posting and perusing through the gtf, just want to confirm.Thanks

ADD REPLY • link 5.5 years ago by Aishwarya Kulkarni ▴ 90

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What if there is no information on a published genome about UTR annotation? For example, i was sure to have extracted also the UTR regions when downloading [Unspliced (Gene) option in Biomart/Ensembl] for a list of genes the gene sequences in bulk. It turned out that those sequences were not annotated. Can somebody tell me how this annotation is performed and why for some genomes have it is released and for others is not ? Is there a way to perform this annotation ex-novo for example for a list of genes of interest? thanks in advance

ADD REPLY • link 4.1 years ago by lessismore ★ 1.4k

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