How to Filter ENSembl to fetch more confident transcripts

Question: How to Filter ENSembl to fetch more confident transcripts

3.0 years ago by

Leuven area (Belgium)

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?

ABLIM1-TSL_example

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

transcripts biomart ensembl • 1.0k views

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modified 3.0 years ago by Emily_Ensembl ♦ 20k • written 3.0 years ago by Stephane Plaisance • 410

3.0 years ago by

Emily_Ensembl ♦ 20k

EMBL-EBI

Emily_Ensembl ♦ 20k wrote:

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.

ADD COMMENT • link modified 3.0 years ago • written 3.0 years ago by Emily_Ensembl ♦ 20k

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.

enter image description here

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

Best Stephane

ADD REPLY • link modified 3.0 years ago • written 3.0 years ago by Stephane Plaisance • 410

Did you try scrolling down the page?

ADD REPLY • link written 3.0 years ago by Emily_Ensembl ♦ 20k

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

One last, what about doing this in R?

ADD REPLY • link written 3.0 years ago by Stephane Plaisance • 410

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

ADD REPLY • link modified 3.0 years ago • written 3.0 years ago by Emily_Ensembl ♦ 20k

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