Hi Gregory, it's simple enough to give bwa a try:
bwa index -a bwtsw genome.fa; bwa aln -l 19 genome.fa primers.fa > temp.sai bwa samse genome.fa temp.sai primers.fa Has actually anyone tried BWA to map primers? I get a lot more results than with blat and blast and have to compare their results now. My problem might be different from Gregory's though as I have ~700k primers to map onto ~60 genomes... PS: Having read the bwa documentation, it seems that the long-sequence alignment mode bwasw in combination with sam2psl.pl might be a nice drop-in replacement for blat... ? cheers Max _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
