Question: BED file for Candida albicans
0
gravatar for skhan
7 months ago by
skhan30
skhan30 wrote:

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.

bed gtf yeast • 279 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by skhan30
1
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k wrote:

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

ADD COMMENTlink written 7 months ago by Jennifer Hillman Jackson25k
1
gravatar for skhan
7 months ago by
skhan30
skhan30 wrote:

Thanks Jen, that was tremendously helpful!

A few things I learned along the way that may be helpful to others:

Thanks again.

ADD COMMENTlink written 7 months ago by skhan30

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/

ADD REPLYlink written 7 months ago by Jennifer Hillman Jackson25k
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