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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
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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