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Old 07-12-2014, 10:40 AM   #1
JonB
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Location: Norway

Join Date: Jan 2010
Posts: 83
Default Extract gene sequences from gff3 file and reference fasta

Hi,

I have a gff3 file and I want to extract the gene sequences (not including introns). Several genes have many isoforms, but I want only the gene sequence (i.e. all the exons spliced). Anyone know of a tool that does this? I tried gffread from the tophat package but I could not get only the gene sequence.

Sample of my gff3 file:
Code:
##gff-version 3
###
scis2053        noncoding       gene    27485   28677   .       -       .       ID=scign013105;Name=scign013105
scis2053        noncoding       mRNA    27485   28677   5921    -       .       ID=scitn013105.1;Parent=scign013105;Name=scitn013105.1
scis2053        noncoding       exon    27485   28677   .       -       .       Parent=scitn013105.1
###
scis673 noncoding       gene    85677   115116  .       +       .       ID=scign002358;Name=scign002358
scis673 noncoding       mRNA    113016  115116  6254    +       .       ID=scitn002358.1;Parent=scign002358;Name=scitn002358.1
scis673 noncoding       exon    113016  113049  .       +       .       Parent=scitn002358.1
scis673 noncoding       exon    113444  114538  .       +       .       Parent=scitn002358.1
scis673 noncoding       exon    114973  115116  .       +       .       Parent=scitn002358.1
scis673 noncoding       mRNA    85677   115099  3835    +       .       ID=scitn002358.2;Parent=scign002358;Name=scitn002358.2
scis673 noncoding       exon    85677   85697   .       +       .       Parent=scitn002358.2
scis673 noncoding       exon    113896  114538  .       +       .       Parent=scitn002358.2
scis673 noncoding       exon    114973  115099  .       +       .       Parent=scitn002358.2
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Old 07-15-2014, 01:13 AM   #2
Delphine
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Location: France

Join Date: Oct 2010
Posts: 2
Default

Hi,

You can use the BEDtools suite with getfasta (http://bedtools.readthedocs.org/en/l.../getfasta.html). You need your gff3 file and the fasta file of your genome (reference).
Usage: bedtools getfasta [OPTIONS] -fi <input FASTA> -bed <BED/GFF/VCF> -fo <output FASTA>
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