Missing annotations in simRat_chrR

[Javier Herrero]

Dear Dent, all

It would appear simRat_chrR has only annotations for repeats. In
particular, genes and CDSs are missing. We have been using Mercator
(Carsten Kemena from the CRG provided us with the data) to run Pecan.
Unfortunately, Mercator relies on gene annotation so chrR has been left
out of the alignments.

Is this an error or is there a reason for not having genes on rat R?

Cheers

Javier

--
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK

[Dent Earl]

This is an oversight on my part, sorry. I'll correct this and message the list in the next day or two.

d

Sent from my iPhone

[Dent Earl]

Hey Javier,

The bed files are all okay, there was small problem with the gffs. As an aside, anyone who is using *only* the gffs should note that they do not contain the repeat masker regions (you can find those in the *.annots.repmask.bed files). I've recreated the gffs for the simulations and verified that the simRat has other annotations:
[dearl@kolossus alignathon]$ grep chrR simRat.annots.gff | awk '{print $3}' | sort | uniq
CDS
NGE
NXE
UTR
island
tandem

I have reposted them:
http://compbio.soe.ucsc.edu/alignathon/data/simMammals.annots.gff.tar.gz
http://compbio.soe.ucsc.edu/alignathon/data/simPrimates.annots.gff.tar.gz

Sorry about that, let me know if there are any other anomalies!

d

[Carsten Kemena]

Dear Dent,

I have to agree with Javier that the CDS annotation for chrR is missing
in the bed files I downloaded. Comparing the bed file and the gff file
for simRat I have about twice as much CDS annotations in the gff file as
in the bed file.

Cheers,
Carsten

[Dent Earl]

Hey Carsten,
You're right, the bed files on the website were wonky too. But no longer! Corrected version:
http://compbio.soe.ucsc.edu/alignathon/data/simMammals.annots.tar.gz

d