Question: Transcript support level in Gencode gtf v19
1
gravatar for aditi.qamra
4.3 years ago by
aditi.qamra260
Toronto
aditi.qamra260 wrote:

Hi,

I am using the gencode v19 gtf file for annotation of my chipseq data ( source - ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/) and the description of the format of the file (http://www.gencodegenes.org/gencodeformat.html) mentions that there is an optional field called transcript_support_level. However I cannot find that information for any of the records in the gtf file nor does any other data file in the release has that information.

Surprisingly though, in the UCSC browser, for all gencode transcripts, the transcript support level has been mentioned ( which to me seems like that there should be a file somewhere that contains this tag). The gtf files from UCSC gencode track/Ensembl FTP also do not contain this record. 

Has anybody used this field before ? and if so how ? Does anybody have an idea on where can I source the data sheet that would contain the transcript support level information ?

Thanks !

 

gencode annotation gtf • 2.7k views
ADD COMMENTlink modified 4.3 years ago by geertvandeweyer0 • written 4.3 years ago by aditi.qamra260
1

At least for access via Ensembl, I vaguely remember this being covered in the most recent webinar. Have a look there first and if it's not mentioned then hopefully Denise will notice this post (if not, one of us can notify her on twitter), since she'd likely know the answer to this.

ADD REPLYlink written 4.3 years ago by Devon Ryan88k
1

Devon - Thanks for the link ! Helped me figure what Emily just confirmed.

 

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by aditi.qamra260
2
gravatar for Emily_Ensembl
4.3 years ago by
Emily_Ensembl17k
EMBL-EBI
Emily_Ensembl17k wrote:

We brought them in for the most recent Ensembl/GENCODE release, which is Ensembl 77/GENCODE 21, so they will not be available in Ensembl 75/GENCODE 19. Also, at present they are not being included in GTF files.

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Emily_Ensembl17k

Emily - Understood, they are not included in the v19 release but I am still surprised to see that annotation in the UCSC browser on transcripts from Gencode v19 track ? (Is it because the http://www.gencodegenes.org/releases/ mention that UCSC has both Grch37 and 38 ?) Can you explain what does that mean.

Also Is there anyway to infer the transcript support level information from the data present in v19 release ?

ps. sorry for all the edits

Thanks !

ADD REPLYlink written 4.3 years ago by aditi.qamra260
1

These have been produced by UCSC for a long time. We decided to incorporate them into Ensembl/GENCODE only recently. You can get them from UCSC separately for older releases.

ADD REPLYlink written 4.3 years ago by Emily_Ensembl17k

Emily - Are TSL values also available through biomart? I can't find them there. 

ADD REPLYlink written 4.3 years ago by geertvandeweyer0
2

Not yet. We're planning on adding them.

ADD REPLYlink written 4.3 years ago by Emily_Ensembl17k
1

TSLs will be available in BioMart in the next release of Ensembl, due next week. More details can be found on our blog post.

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by Denise - Open Targets4.8k

Hi Emily/Denise: Does TSL information included in GTFs yet?  I tried GRCH37.82 GTFs could not find them

ADD REPLYlink written 3.1 years ago by Rm7.8k
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