Extract exon sequence based on GFF3 end FASTA #3
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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. |
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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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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.1ACTGTGACA......>Eucgr.A00001.1.v2.0.exon.2ACTGTGACA......>Eucgr.A00001.1.v2.0.exon.3ACTGTGACA......(...)>Eucgr.A00001.1.v2.0.exon.12ACTGTGACA......(...)Could you help me?
Thank you so much!
sample_GFF3_tsv.txt
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