Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
Something wrong in FlyBase's gtf (gff to gtf conversion) saskak Bioinformatics 4 11-27-2015 12:40 PM
Error with GTF file when using htseq-count MDonlin Bioinformatics 13 01-13-2015 08:29 AM
Need advice: want to create a gtf file of transcript sequences JonB RNA Sequencing 0 08-29-2013 11:27 AM
Create GTF or GFF3 file from draft genome bernardo_bello Bioinformatics 3 12-23-2012 07:51 PM
GFF to GTF, and GTF to GRanges objects lewewoo Bioinformatics 2 04-03-2012 02:52 PM

Thread Tools
Old 10-05-2016, 07:11 PM   #1
Junior Member
Location: Brazil

Join Date: Oct 2016
Posts: 2
Default How to create a GTF/GFF file for HTSeq OR how to count reads without GTF?

I am working with RNAseq of an insect under different treatments. I already have the data (Illumina HiSeq paired-end reads) and I was planning to follow the protocol from Anders et al. (2013) to analyze it (I already did it in the past with a model organism). However, the genome of this insect was recently sequenced, so it still has no GTF file available. The only files available are: the genome.fasta and the CDS.fasta.

So far, I mapped the reads on the genome using tophat (without providing a GTF file) which provided me bam/sam files. Now, I should count the reads per gene using HTSeq. However, the input for HTSeq is a GTF file that I dont have.

How can I count reads per gene without a GTF file? Is it possible to use the genome and the CDS to create a GTF/GFF file for HTSeq?

Any other idea on how to proceed would be helpful.
Thank you so much!
Biol is offline   Reply With Quote
Old 10-05-2016, 09:39 PM   #2
Persistent LABS
Location: Pune, India

Join Date: Apr 2016
Posts: 20

Hi Biol,
If you want to analyze your data using the pipeline HTSeq->DESeq2, you will require GTF file, and in your case probably you can write a script to create one based upon the alignment of CDS.fasta to your genome.fasta.
But if you are willing to use other pipeline, you can use TopHat->Cufflinks->Cuffmerge->Cuffdiff. Here, the reference annotation is not mandatory.
Persistent LABS
Persistent LABS is offline   Reply With Quote

gtf, htseq, tophat

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 05:05 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO