Hi there,
Does anyone know where I can get, or how I can generate, a BED file (or GTF file) for Candida albicans (strain SC5314, assembly version 22)?
The current assembly is here but I'm not sure how to generate a BED file from the data there:
http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly22/current/
Thanks.
Hello,
The data source provides the fasta sequence for features but apparently does not provide the reference annotation (coordinates) of those features with respect to the reference genome. I checked the fasta headers and this info isn't even recorded there. They should have this data somewhere. Maybe write them and ask?
Or, use an alternative source. Genbank has the assembled genome along with the reference annotation. https://www.ncbi.nlm.nih.gov/genome/?term=Candida+albicans%5BOrganism%5D
Hope that helps! Jen, Galaxy team
Thanks Jen, that was tremendously helpful!
A few things I learned along the way that may be helpful to others:
the candidagenome.org FASTA contains diploid info + sequence for what I think is the mitochondrial genome (chrM); the GenBank genome contains haploid sequences and no mitochondrial genome
the candidagenome.org GFF and GTF data is housed here: http://www.candidagenome.org/download/gff/C_albicans_SC5314/Assembly22/
Thanks again.
Thanks for posting back! Also very helpful :)
And the mito not being included with the primary organism chromosomes is common at Genbank. Sometimes these are added as a link to another bioproject or accession in the header, other times a search is needed to locate the target accession (when it exists). This can be true for mitochondria, chloroplast, and plasmid sequence.
In short, the different content needs to be found, loaded to Galaxy, merged (concatenated), and then run through the tool NormalizeFasta before use.
Custom genome FAQ: https://galaxyproject.org/learn/custom-genomes/
