Show sample genome on Jbrowse
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6.0 years ago
Whoknows ▴ 890

Hi

I downloaded Jbrowse and I want to use this for a sample genome with size near 3Gb and a gff file.

I looked closely to its tutorial and its Wiki website but it did not help.

Is anybody know a pipeline for simple adding fasta file and gff to Jbrowse ?

Thanks

jbrowse fasta gff • 1.8k views
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JBrowse's Setup tutorial isn't bad. Your question really sounds like "Can someone set this up for me?". I think you should expand your question with what you've tried so far, and what isn't working specifically.

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5.9 years ago
Whoknows ▴ 890

I got the answer and pipeline for JBrowse,

A) Installation ( first be sure of apache2 path) then use root mode :

  1. cd /var/www (in number of Linux path is /var/www/html)
  2. unzip JBrowse-full-1.4.1.zip
  3. cd JBrowse-full-1.4.1
  4. ./setup.sh

B) Configuration fasta file and GFF for JBrowse, just run these commands:

You should run following commands separately for each chromosome.

  1. bin/prepare-refseqs.pl --fasta Sample.fasta

  2. bin/flatfile-to-json.pl --gff Sample.gff --tracklabel Sample_Annotation

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