question about the quality when mapping with gmap

[lixiangru]

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.

[doliv071]

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.