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Question: Select a reference genome
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gravatar for cucucucoco
14 months ago by
cucucucoco • 0
cucucucoco • 0 wrote:

HI! i wonder what mean hg19? hg38?

I want to mapping ro HIV-1 virus genome or infected HIV-1 cell. so What i sselect reference genome?

and i dont know, normal hg19 and hg19 Canonical what different are?
rna-seq alignment bowtie • 675 views
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modified 14 months ago by Jennifer Hillman Jackson ♦ 25k • written 14 months ago by cucucucoco • 0
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gravatar for Jennifer Hillman Jackson
14 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The genomes hg19 and hg38 are sourced from UCSC. Full release details (and data) are included here: http://hgdownload.soe.ucsc.edu/downloads.html#human

The genome hg19 Canonical is the same as hg19 except that it only includes the autosomes, the sex chromosomes, and the mitochondrial genome. Haplotype chromosomes and unknown/unmapped contigs are excluded.

For the HIV-1 genome, upload it to Galaxy and use it as a custom genome/build.

Hope this helps! Jen, Galaxy team
ADD COMMENT • link written 14 months ago by Jennifer Hillman Jackson ♦ 25k

Thank you. but i got one more question. if i have to use HIV-1 genome using custom genome/build section, what form is available? Fast -A?? i downloaded in NCBI to FastA file. (https://www.ncbi.nlm.nih.gov/nuccore/AF033819) was it right??? if i want to annotate about HIV-1 NCBI dataset. how can i annotate ???? please help me..

ADD REPLY • link written 14 months ago by cucucucoco • 0

Did you see the help for Custom genomes? It explains the expected format and how to reformat as needed plus has examples for setting tool forms to use the custom genome fasta dataset as a mapping target with tools.

Definitely use the NormalizeFasta tool on data from NCBI (the options are explained in the same custom genome FAQ). The identifiers are formatted like this by default:

>AF033819.3 HIV-1, complete genome

But they need to be reformatted to be like this for use in Galaxy:

>AF033819.3

The genome you linked is the primary HIV-1 genome. Use the "Send to" menu at NCBI to export the fasta data locally to your computer, then upload it to Galaxy.

The NCBI "Send to" options should be set like this: https://imgur.com/a/5S61x

Uploading to Galaxy is explained here: Loading Data

ADD REPLY • link written 14 months ago by Jennifer Hillman Jackson ♦ 25k
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