Extract exon sequence based on GFF3 end FASTA

[marcelolaia]

Hi, after a hard search on the net I found this awesome script. It works nice. However, I need to extract all exon sequence from a genome based on GFF3 and FASTA. Please, found attached a GFF3 sample file.
From that file I need to extract these sequences:
>Eucgr.A00001.1.v2.0.exon.1
ACTGTGACA......
>Eucgr.A00001.1.v2.0.exon.2
ACTGTGACA......
>Eucgr.A00001.1.v2.0.exon.3
ACTGTGACA......
(...)
>Eucgr.A00001.1.v2.0.exon.12
ACTGTGACA......
(...)
Could you help me?
Thank you so much!

sample_GFF3_tsv.txt

[isugif]

You might be looking for the gff2fasta.pl script located here: https://github.com/ISUGIFsingularity/utilities/tree/master/utilities Please let me know if that is the case.

[marcelolaia]

On 23/04/20 at 05:29, Andrew Severin wrote: You might be looking for the gff2fasta.pl script located here: [1]https://github.com/ISUGIFsingularity/utilities/tree/master/utilities Please let me know if that is the case.

Hi Andrew, Thank you for promptly replay. I found that script on Biostar forum. I run it and got the files. However, the output.exon.fasta [1] don't much the exons in the GFF3 [2]. Please, could you help me? For exemple: Inside GFF3 file are: Chr01 phytozomev10 exon 2787014 2787767 . - . ID=Eucgr.A00001.1.v2.0.exon.12;Parent=Eucgr.A00001.1.v2.0;pacid=32049109 Chr01 phytozomev10 exon 2787803 2787834 . - . ID=Eucgr.A00001.1.v2.0.exon.11;Parent=Eucgr.A00001.1.v2.0;pacid=32049109 Chr01 phytozomev10 exon 2788190 2788300 . - . ID=Eucgr.A00001.1.v2.0.exon.10;Parent=Eucgr.A00001.1.v2.0;pacid=32049109 Chr01 phytozomev10 exon 2789313 2789399 . - . ID=Eucgr.A00001.1.v2.0.exon.9;Parent=Eucgr.A00001.1.v2.0;pacid=32049109 Chr01 phytozomev10 exon 2789765 2789884 . - . ID=Eucgr.A00001.1.v2.0.exon.8;Parent=Eucgr.A00001.1.v2.0;pacid=32049109 Chr01 phytozomev10 exon 2789985 2790162 . - . ID=Eucgr.A00001.1.v2.0.exon.7;Parent=Eucgr.A00001.1.v2.0;pacid=32049109 Chr01 phytozomev10 exon 2790477 2790694 . - . ID=Eucgr.A00001.1.v2.0.exon.6;Parent=Eucgr.A00001.1.v2.0;pacid=32049109 Chr01 phytozomev10 exon 2790774 2790880 . - . ID=Eucgr.A00001.1.v2.0.exon.5;Parent=Eucgr.A00001.1.v2.0;pacid=32049109 Chr01 phytozomev10 exon 2790969 2791089 . - . ID=Eucgr.A00001.1.v2.0.exon.4;Parent=Eucgr.A00001.1.v2.0;pacid=32049109 Chr01 phytozomev10 exon 2791278 2791373 . - . ID=Eucgr.A00001.1.v2.0.exon.3;Parent=Eucgr.A00001.1.v2.0;pacid=32049109 Chr01 phytozomev10 exon 2791468 2791696 . - . ID=Eucgr.A00001.1.v2.0.exon.2;Parent=Eucgr.A00001.1.v2.0;pacid=32049109 Chr01 phytozomev10 exon 2792210 2792340 . - . ID=Eucgr.A00001.1.v2.0.exon.1;Parent=Eucgr.A00001.1.v2.0;pacid=32049109 However, gff2fasta.pl script retrive only one exon, instead 12, for gene Eucgr.A00001.1.v2.0. Thank you so much! 1. https://www.dropbox.com/s/dicbsvo7hsuznq5/output.exon.fasta?dl=0 2. https://www.dropbox.com/s/b8ge28sa6nwcuhl/Egrandis_297_v2.0.gene_exons.gff3?dl=0 3. Reference genome (~700 MB) https://www.dropbox.com/s/4p0mxqak9erjil8/Egrandis_297_v2.0.fa?dl=0

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-- Laia, ML https://publons.com/researcher/1755871/ http://orcid.org/0000-0001-6366-4558