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08-09-2016, 03:16 AM
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#1 |
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Member
Location: Europe Join Date: Feb 2013
Posts: 58
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Different alignment rate of Tophat with and without GTF file
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 |
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08-09-2016, 04:24 AM
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#2 |
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Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 7,087
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| rna sequencing, tophat |
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