How to Filter ENSembl to fetch more confident transcripts

Question

[Stephane Plaisance]

We recently noted that the current ENSembl data is full of very short isoforms that likely do not represent functional transcripts BUT lead to over-estimate the diversity of the transcriptome (and may include intron-retention isoforms too).

I am looking for a programatic way to reproduce a subset of ENSembl closer to what is provided in ENCODE but that would let me control the degree of evidence I wish to keep.

I found info in ENSembl about TSL (Transcript Support Level) but do not find TSL exposed in BioMART not examples of [R] biomaRt commands applying this annotation to filtering (# although head(organismAttributes("Homo sapiens"), 20) returns transcript_tsl at position #15)

Does anybody have code biomaRt examples to fetch only human transcripts with annotation 'GENCODE basic' as exemplified in the screen-shot of the ABLIM1 gene?

Getting the full GENCODE build as a download is not what I need here, I want to create my own subsets

Thanks in advance

Stephane

Answer 1

[Emily]

TSL and GENCODE Basic are both filters available in BioMart. They're listed under GENE.

Also, please do not cross-post to BioStars and to Ensembl helpdesk, as we monitor both of these channels. I will close your ticket on Ensembl helpdesk.

[Stephane Plaisance]

Thanks for this Emily,

Can you please be more explicit, I do not see GENCODE nor TSL in the drop down under gene in BioMART.

Also, what about my specific request to do this programatically using biomaRt in R?

Best Stephane

[Emily]

Did you try scrolling down the page?

[Stephane Plaisance]

SHAME on ME :-) is t is clearly Friday.

One last, what about doing this in R?

[Emily]

filters = 'transcript_tsl', values = TRUE,
filters = 'transcript_gencode_basic', values = TRUE