Hi,
I have some Illumina paired end genomic reads from a plant species without a genome sequence, so I wanted to align them to a related genome. I tried using bowtie ( --seedmms 3 --maqerr 250) but I am getting very few alignments (<5% paired ends, and ~10% for each end separately). I tried to use the -v option to increase the mismatches but the limit seems to be 3 (same as the seed mismatches acc to the manual). I guess my genetic distance is too great...
Do people have a preferred aligner when aligning to a reference from another species, or would I be better off assembling the reads de novo and aligning them afterwards?
Thanks, SD
I have some Illumina paired end genomic reads from a plant species without a genome sequence, so I wanted to align them to a related genome. I tried using bowtie ( --seedmms 3 --maqerr 250) but I am getting very few alignments (<5% paired ends, and ~10% for each end separately). I tried to use the -v option to increase the mismatches but the limit seems to be 3 (same as the seed mismatches acc to the manual). I guess my genetic distance is too great...
Do people have a preferred aligner when aligning to a reference from another species, or would I be better off assembling the reads de novo and aligning them afterwards?
Thanks, SD
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