Next steps:
- Create HELP ticket containing user's email send to Ann and link it to this one (it will still be protected)
- Google search to see if more recent assemblies can be found.
I found this paper that appears to be a newer, better version for Daphnia magna, but I don't know if the data can be obtained:
Depending on above, create a new ticket for assembling the Quickload files for the two Daphnias:
BED-detail file with:
- Human-friendly text functional annotations in field 14
- Gene name in field 13
- Transcript name in field 4
Two-bit file with genome sequence
- Reference sequence names should match reference sequence names used in BED-detail file above
genome.txt file with reference sequences and sizes from 2bit file above
- Reference sequences should be listed in a user-friendly order; depends on how the sequences are named and the completeness of the genome
Also, if the genome(s) are very much in fragments and there are tens of thousands of sequences per assembly, we need to do some filtering to screen out reference sequences that lack annotations or are extremely small. This requires some research to find out how many is too many – i.e., how long does it take the gene models to load into IGB.
Daphnia pulex assembly version 1.0 (February 2011)
From Ensembl: https://metazoa.ensembl.org/Daphnia_pulex/Info/Index
Assembly:
ftp://ftp.ensemblgenomes.org/pub/metazoa/release-44/fasta/daphnia_pulex/dna/Daphnia_pulex.V1.0.dna.toplevel.fa.gz
Annotation:
ftp://ftp.ensemblgenomes.org/pub/metazoa/release-44/gff3/daphnia_pulex/Daphnia_pulex.V1.0.44.gff3.gz
Daphnia magna assembly version daphmag2.4 (April 2010)
From Ensembl: http://metazoa.ensembl.org/Daphnia_magna/Info/Index?db=core
Assembly:
ftp://ftp.ensemblgenomes.org/pub/metazoa/release-44/fasta/daphnia_magna/dna/Daphnia_magna.daphmag2.4.dna.toplevel.fa.gz
Annotation:
ftp://ftp.ensemblgenomes.org/pub/metazoa/release-44/gff3/daphnia_magna/Daphnia_magna.daphmag2.4.44.gff3.gz