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Question: tophat reference genome
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gravatar for humairawahid
2.6 years ago by
humairawahid • 0
humairawahid • 0 wrote:

Kindly add the genome of Pinus taeda and Picea glauca to the tophat reference genome as I am unable to upload large genome files through FTP, Thank you very much!
request genome database custom • 685 views
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modified 2.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.6 years ago by humairawahid • 0
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gravatar for Jennifer Hillman Jackson
2.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

For Pinus taeda, use the assembly GCA_000404065.2 ? The genome.fna.gz is 5.3 GB compressed and should load by FTP. ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000404065.2_Ptaeda1.01

For Picea glauca, use the assembly GCA_000411955.5 ? The genome.fna.gz is 5.5 GB compressed and should load by FTP. ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000411955.5_PG29_v4.1

Both are still scaffold-level assemblies and may or may not function optimally with certain tools, but you can test this out. If the load times out when using an FTP client (Filezilla is one), it can be resumed to finish the transfer.

I added both to the list of genomes to consider adding. This will not be immediate. https://github.com/galaxyproject/galaxy/issues/1470

Custom reference genome help link below. Be sure to note the chromosome naming advice for the fasta. In short, keep these very simple by using only an alphanumeric plus underscores identifier, with no description content. https://wiki.galaxyproject.org/Support#Custom_reference_genome
ADD COMMENT • link modified 2.6 years ago • written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k
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