Hi all, I’m interested in looking at many different versions of the c elegans genomic data to learn something about the genetic variation in the population.
I’ve been exploring the ftp site: ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/sequence/genomic/ and I’ve noticed that many of the genomic fasta files are identical.
For example, c_elegans.PRJNA13758.WS238.genomic.fa and c_elegans.PRJNA13758.WS239.genomic.fa are exactly the same. Were these literally sequence from the same cell or same member of the species?
If so, how do I go about obtaining genomic data from different members of the species. Thanks so much for your help.
that is because that part of the FTP site shows all files per species of the all releases.
As you want only the files of a particular release (say WS257), try that one: ftp://ftp.wormbase.org/pub/wormbase/releases/WS257/species/
And if you look at http://www.wormbase.org/species/c_elegans#032--10 , you can see that the C.elegans genome hasn’t been changed since WS235. So all genomic fasta files for C.elegans from 235-257 should be the same (potentially with small variations in the repeat masking).
For C.elegans there are currently only two genomes available at WormBase : one for the reference strain (N2 / PRJNA13758) and one for the Hawaiian strain (CB4856 / PRJNA275000)
In addition SNPs from environmental sequencing are found as variations to the N2 genome in the GFF files.