database for reference genome

Question

[StudentBio]

hello the community please I am looking for a database where I can retrieve the date palm reference genome,I want to map my reads to get out the variations.

[lieven.sterck]

hi,

let me google that for you ...

(aka, what have you tried already? or where did you look for it?)

[StudentBio]

I tried genome database in ncbi but when we wanted to visualize the results of the mapping on igv I received an error that no alignment was made

[GenoMax]

Not finding the genome and not being able to visualize your mapped results in IGV are two completely different things. You will need to create a custom genome in IGV using the same genome file that you used to do the alignments. Instructions for creating custom genomes in IGV are available here.

[lieven.sterck]

I might be mistaken but are there not already several (2?) date palm genomes published? or was that oil palm?

[StudentBio]

i don t understand can you explain please

[lieven.sterck]

just make sure you get the reference (and version) you expect to get. If there are several date palm genomes available you might run into confusing situations

Answer 1

[lakhujanivijay]

Hi

I could find that on NCBI genome here

Look at this paper

[StudentBio]

please can you accept my request on LinkedIn <link removed>

[Emily]

Please do not stalk people outside of BioStars. People here offer their help at their convenience.

Answer 2

[Benn]

What about here? DRDB (Date palm Resequence Database).

Answer 3

[vmicrobio]

Hello,

You may retrieve your reference genomes using esearch, with something like this:

.../edirect/esearch -db nucleotide \
        -query "name_of_your_organism[organism] AND genome[title]" \
    | .../edirect/efetch -format fasta > references.fasta

Answer 4

[5heikki]

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/413/155/GCA_000413155.1_DPV01