Display translations of CDS from transcript.gtf

[Bjorn Kafsack]

I'm working with S. cerevisiae RM11-1a sequencing results. 

I've had no problem loaded generating an RM11-1a .genome file from the supercontig fasta file and transcripts.gfp file from http://www.broadinstitute.org/annotation/genome/saccharomyces_cerevisiae.3/MultiDownloads.html

But what I'm still missing is the translations of CDS contained in the gtf files similar to how gene translations show up when you load the SacCer3 reference genome.

I'm looking for any of these options

a) An already existing RM11-1a .genome file with gene/transcripts containing gene translations in the gene track

b) a setting in igv that translates CDS in gtf files

c) a tool that adds translations to the gtf files using the reference genome fasta + the CDS positions from the gtf

d) any format that will allow me to load translations as an annotation in igv since i can use existing data to combine translations and positions.

Thank you in advance

Björn

[Bjorn Kafsack]

BUMP

[James Robinson]

Apologies, we are short -staffed and I haven't had time to investigate GTF options.  I know for sure gff3 works, at least when using the gene model e ample on the Sanger site.  Have you tried gff3?

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[Bjorn Kafsack]

Thanks for getting back to me Jim,

I can't for the life of me find RM11-1a annotations (including the gff3 files). I've looked in ensembl & at the Saccharomyces Genome Resequencing Project for them.

I've had success in getting the translations to show by reformatting the .gtf file i had. 

What I'm still trying for is to get the amino acid number in the CDS to be included in the pop up bubble for the genes track as it does for sacCer3 (See attached images).

AA number shows up in the bubble if I load just the sacCer3 fasta file as a genome followed by the ensGene file in the sacCer3 .genome package as a regular file.

I guess igv can calculate aa number if the annotations are in the ensGene but not gff3.

(see http://moma.ki.au.dk/genome-mirror/cgi-bin/hgTables?hgsid=12007&hgta_doSchemaDb=dm3&hgta_doSchemaTable=ensGene )

I'll try converting the gff3 to ensGene unless you have a better suggestion or know of a tool that does that.

Thanks

Björn

On Tuesday, July 22, 2014 4:41:11 PM UTC-7, Jim Robinson wrote:

Apologies, we are short -staffed and I haven't had time to investigate GTF options.  I know for sure gff3 works, at least when using the gene model e ample on the Sanger site.  Have you tried gff3?

On Thursday, July 10, 2014, Bjorn Kafsack <bkaf...@gmail.com> wrote:

I'm working with S. cerevisiae RM11-1a sequencing results. 

I've had no problem loaded generating an RM11-1a .genome file from the supercontig fasta file and transcripts.gfp file from http://www.broadinstitute.org/annotation/genome/saccharomyces_cerevisiae.3/MultiDownloads.html

But what I'm still missing is the translations of CDS contained in the gtf files similar to how gene translations show up when you load the SacCer3 reference genome.

I'm looking for any of these options

a) An already existing RM11-1a .genome file with gene/transcripts containing gene translations in the gene track

b) a setting in igv that translates CDS in gtf files

c) a tool that adds translations to the gtf files using the reference genome fasta + the CDS positions from the gtf

d) any format that will allow me to load translations as an annotation in igv since i can use existing data to combine translations and positions.

Thank you in advance

Björn

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[Jim Robinson]

Hi Bjorn,

I did a little research on these formats and have some news, not good news for you but at least more information.   IGV does not try to interpret amino acids unless the frame-shift is specified for a coding section.    Just counting in groups of 3 from the start codon does not always work,  there are missing bits and other problems in some annotation files that throw this off.   Not all formats have provision for specifying frameshift,  gff3 and some of the UCSC gene table formats do.   

You mention converting gff3 to ensgene, that should not be necessary if your gff3 file specifies frameshift.   If you want to attach a small sample of the gff3 file I will see if I can get it to work.

Jim