13-Feb-2015

Correction to GFF files for some species:
===================================================

The GFF files for the following species have been replaced.
- SMP (Schistosoma mansoni)
- NECAME (Necator americanus)

For SMP, the reason was some inconsistency with some gene models, and lack of phase info on all CDSs.
For NECAME, the reason was inconsistent naming of scaffold names, not matching the respective assembly fasta file.

The new GFFs come from WormBase Parasite, release 1, without any modification:
- ftp://ftp.ebi.ac.uk/pub/databases/wormbase/parasite/releases/WBPS1/species/schistosoma_mansoni/PRJEA36577/schistosoma_mansoni.PRJEA36577.WBPS1.annotations.gff3.gz
- ftp://ftp.ebi.ac.uk/pub/databases/wormbase/parasite/releases/WBPS1/species/necator_americanus/PRJNA72135/necator_americanus.PRJNA72135.WBPS1.annotations.gff3.gz

These match the data that was used for our 50HGP Ensembl Compara database.

The previous versions of the GFF files for these species are kept here.
Only GFF files were modified/replaced and not the other files (e.g. assembly, protein.fa)
I have also modified the name of the SMP GFF from SMP.gff to SMP.gff3, to match file naming of the other species

The 'old' GFFs were stored on ARCHIVE/REPLACED.GFFs

Diogo Ribeiro, dr7@sanger.ac.uk, 13-Feb-2015


Removal of erroneous GFF files for some species:
===================================================

The GFF files for the following species have been removed from this folder:
- CGI (Crassostrea gigas)
- H044 (Panagrellus redivivus)
- IscaW1 (Ixodes scapularis)
- NEMVE (Nematostella vectensis)
- PRIPAC (Pristionchus pacificus)

Note that all of these come from external sources, not part of the 50HGP sequenced species.
The reason is that in these files all gene, mRNA and exon (possibly other types) of entries had wrong coordinates, the start position matching the end position. This did not affect CDS entries.
The 'old' GFF files that were on this folder were backed up on ARCHIVE/REMOVED.GFFs
A correct GFF file for these species, created by dumping the 50HGP Ensembl Core (Compara) database are provided here on ARCHIVE/REMOVED.GFFs/ensembl_dump_files

Diogo Ribeiro, dr7@sanger.ac.uk, 13-Feb-2015