Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
Creating a mRNA GTF file from fasta for HTSeq ? CEPHSeq Bioinformatics 11 06-18-2015 09:44 AM
GFF to fasta (intergenic regions and introns) gaby Bioinformatics 25 10-27-2014 04:54 AM
Reads clipping by refernce coordinates? shiningway Bioinformatics 3 04-08-2014 07:43 AM
how to convert gff and fasta file to genbank format vivienne_lovely Bioinformatics 4 03-20-2014 05:23 PM
How do I go from a fasta and a chromosome to gtf/gff file? Brown_lineage Bioinformatics 8 12-07-2012 06:21 AM

Thread Tools
Old 10-28-2014, 03:51 AM   #1
Location: Europe

Join Date: Feb 2013
Posts: 58
Default creating GFF file from refernce fasta


I am working a flatworm for which the reference genome is not well characterized. I found the refernece trancriptome for my species from internet and I mapped my reads to refernce trancriptome. Now I want count the reads but I couldnt find the GFF file for this trancriptome. How can I count the reads without GFF file? is it possible genrate a GFF file for this trancriptome.

Kindly guide me
dena.dinesh is offline   Reply With Quote
Old 10-30-2014, 04:29 PM   #2
I like code
Location: San Diego, CA, USA

Join Date: Sep 2009
Posts: 436

I'm assuming you're dealing with some type of standard RNA-seq (illumina) type data. Typically when people use a GFF file to count reads the alignments were made against a genome and not a transcriptome. Because of the ambiguous nature of transcriptomes I recommend looking into RSEM, Sailfish or eXpress for your read count/expression quantification. Each of those software use an EM based algorithm to disambiguate the assignment of reads to each transcript. This seems to work fairly well even when dealing with fairly complex gene loci (i.e. many alternative isoforms). Be warned that what this will produce is isoform level expression so if your reference transcriptome contains multiple isoforms per gene there will be some additional uncertainty in this output. eXpress is nice in that it will generate a confidence interval on the FPKM values it produces so you can get an idea of those transcripts that it cannot confidently call. To the best of my knowledge the art of differential expression at the isoform level has not been fully developed though the EBSeq package claims to be able to do it.
/* Shawn Driscoll, Gene Expression Laboratory, Pfaff
Salk Institute for Biological Studies, La Jolla, CA, USA */
sdriscoll is offline   Reply With Quote

counting, gff, rnaseq mapping

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 01:15 AM.

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