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This isn't a direct answer to your question, but I recently performed alignment of PacBio long-reads using both GMAP and STAR. For the alignment I gave GMAP the fasta and I gave STAR the fastq. They performed almost identically. I was only looking for splice variants and differential expression so I was not concerned with SNPs or other such variants which may not be possible to detect without base quality data. -
question about the quality when mapping with gmap
Hi,all!
Does gmap account for the sequencing quality when mapping?
It seems that no argument is for the quality file when the cDNA file is in fasta format. So I wonder whether gmap account for the base quality.
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