SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
fastx_quality_stats error : input file (-) has unknown file format mbk0asis Bioinformatics 5 01-20-2014 04:03 PM
Input file format for RSEM edge Bioinformatics 1 09-20-2012 05:33 AM
Artemis acceptable input file format problem edge Bioinformatics 13 07-19-2012 03:58 PM
Correct input file format for SLOPE? Heisman Bioinformatics 2 09-21-2011 06:20 AM
csfasta files - miRanalyzer input file format naluru SOLiD 0 12-09-2010 08:55 AM

Reply
 
Thread Tools
Old 05-12-2014, 02:17 PM   #1
capricy
Senior Member
 
Location: 63130

Join Date: Apr 2012
Posts: 125
Default DNAPlotter input file format

I downloaded and installed DNAplotter. According to their instructions, it accepts a variety of file format types including GFF3.

I have a GFF3 as following:

=========
##gff-version 3
##sequence-region Scaffold122 1 3799748
# Gene gene:L3E_00178
Scaffold122 SNAP gene 1272634 1272964 . - . ID=gene:L3E_00178;Name=L3E_00178;Note=Hypothetical protein;public_name=L3E_00178
Scaffold122 SNAP mRNA 1272634 1272964 . - . ID=transcript:L3E_00178;Parent=gene:L3E_00178;Name=L3E_00178;info=position:1272634-1272964 method=Hypothetical protein
Scaffold122 SNAP exon 1272634 1272814 18.993 - . ID=exon:L3E_00178.1;Parent=transcript:L3E_00178
Scaffold122 SNAP exon 1272888 1272964 13.225 - . ID=exon:L3E_00178.2;Parent=transcript:L3E_00178
Scaffold122 SNAP CDS 1272634 1272814 . - 2 ID=cds:L3E_00178;Parent=transcript:L3E_00178
Scaffold122 SNAP CDS 1272888 1272964 . - 0 ID=cds:L3E_00178;Parent=transcript:L3E_00178
===========

I launch DNAplotter: java -jar DNAPlotter.jar

and tried to visualize this gff3 file

however, got the error messages:
while reading from dnaplotter.gff3: gene can't have public_name as a qualifier
while reading from dnaplotter.gff3: mRNA can't have info as a qualifier

Could anybody give some DNAplotter input examples so that I can format my file accordingly?

Thanks a lot for the help.

Capricy
capricy is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:08 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO