Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
cufflinks : analysis comparison with and without a gtf reference file sohnic Bioinformatics 3 07-07-2019 05:40 AM
cuffdiff Error: cannot open reference GTF file L for reading crh Bioinformatics 4 04-14-2014 01:52 PM
GTF file with gene name attribute for Cuffcompare ChrisL Bioinformatics 15 04-15-2013 07:21 AM
GTF file for reference of human transcriptome oxydeepu Bioinformatics 1 05-25-2012 03:09 AM
tophat -G gene model annotations GTF format? silin284 Bioinformatics 15 04-21-2011 06:26 AM

Thread Tools
Old 06-02-2012, 09:22 AM   #1
Junior Member
Location: new delhi

Join Date: May 2012
Posts: 3
Default entamoeba histolytica reference genome (gene annotation file) in GTF format

I am working with Entamoeba data. I have downloaded the genome data of entamoeba from NCBI in genebank format but did not get in GTF format. I have searched it in UCSC genome browser but unable to find out. Can any one suggest me in either find out it in GTF format or converting from genebank t GTF format ?
paula123 is offline   Reply With Quote
Old 06-04-2012, 02:39 AM   #2
Senior Member
Location: Berlin

Join Date: Jul 2011
Posts: 156

If you are able to do a bit of Python coding on your own you could use the bcbio BioPython module for GFF parsing/writing from the following page; there is a description on how to convert GenBank flat format annotation files into GFF3:

Then you could use the GenomeTools ( gff3_to_gtf tool to get proper GTF (if necessary, many tools can use GFF3 as well).
I've done this before though I've seen troubles with certain GenBank files, as some features are difficult to correctly translate into GFF3. You might need to manually check that the contents are correct, or filter out stuff that isn't needed in the end, to avoid problems with the GenomeTools converter.
arvid is offline   Reply With Quote

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 12:54 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO