What happened?

Hi.

gget seq any-ensembl-transcript returns the genomic sequence spanned by the transcript instead of the transcript sequence. I'm running gget 0.29.3 but this is not recent. I've tried multiple species, long and short transcripts, etc., and the result is the same. It looks like you're taking the last sequence returned by Ensembl by default.

For example, ENST00000589042 (TTN) is 108Kb long. gget seq ENST00000589042 returns a sequence of 280Kb, which matches the span of the genomic locus.

ENST00000229239 (GAPDH) is 1285 nt long. If I download it manually and deselect everything except cDNA, I get a sequence of the right length:

The output from gget seq ENST00000229239 is 3855 nt:

Thanks.

gget version

0.29.3

Operating System (OS)

Linux

User interface

Command-line

Are you using a computer with an Apple M1 chip?

Not M1

What is the exact command that was run?

`gget seq ENST00000589042`

Which output/error did you get?

See above.