[Feedback] Site Feedback: conversion table and typing error

[feedback at gramene.org]

URL         : 

Subject     : Site Feedback: conversion table and typing error

Name        : Hilde Nelissen

Email       : hinel at psb.ugent.be

Organization: UGent/VIB

Comments    : 

Dear,

we are very pleased with the new version of the genome and we were already implementing v4 into our pipelines, but we ran into some issues we would like to address/discuss with you:

a) Is it possible to make a file available, containing the mapping between gene identifiers of the previous annotation and the current annotation? There is an assembly converter available on the Gramene website, but it would be of extremely valuable to the community if a mapping file (from GRMZM to ZM ids) were to be made publicly available as well. We do of course understand that such a mapping is not always possible due to changed gene structures (gene fusions, gene splits, changed exon-intron structure, etc.. ). In addition, if one clicks on the genes in gene-track, you end up on either the annotation from v3 or v4, but there is no link between the two.

b) The GFF file available on the Gramene FTP site (ftp://ftp.ensemblgenomes.org/pub/plants/release-32/gff3/zea_mays/Zea_mays.AGPv4.32.gff3.gz ) is inconsistent with current practices with regard to the naming of features, probably due to a typing error. Every coding transcript is flagged with feature miRNA instead of mRNA. Although the comment-field does indicate that these transcripts are indeed protein coding (through the flag 'biotype=protein_coding' ), it is confusing that the main feature of these transcripts is indicated as miRNA. We assume this to be an error in the output script, which should be easily adjusted.

it would really help our research if you could solve especially the first point! Let us know if you need more information!

thanks a lot!

H.

http://www.warelab.org/bugs/view.php?id=5474