Different alignment rate of Tophat with and without GTF file

dena.dinesh

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Different alignment rate of Tophat with and without GTF file

08-09-2016, 02:16 AM

Hi,

I am new to RNA seq analysis. I am working on non-model organism. I have Genome and de-novo-assembled transcriptome. Using PASA I mapped the transcriptome to genome and obtained GTF file.

When I mapped my RNAseq reads to Genome using tophat by providing GTF file obtained from PASA, I get overall alignment rate of 91.4% while when ran Tophat without GTF option, I got overall alignment rate of 78%.

Why is the difference. Kindly guide me
Tags: rna sequencing, tophat
GenoMax

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Join Date: Feb 2008

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08-09-2016, 03:24 AM

TopHat with and without GTF - SEQanswers

http://seqanswers.com/forums/showthread.php?t=40516

Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc
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Different alignment rate of Tophat with and without GTF file

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