Hi all, It is my understanding that blastn is more sensitive (and thus finds more hits) than megablast (see here and here). However, when I compared my results from running blastn vs. megablast with the same exact inputs and parameters, I got 0 hits for blastn and thousands of matches for megablast (with e-value less than 0.001).
This seems really strange to me and I was wondering if anyone can think of a specific case in which megablast picks up hits that blastn can't pick? These are the commands I ran:
blastn -query unique_31mers.fa -db Homo_sapiens.GRCh37.dna.primary_assembly -outfmt "6 delim=\t" -task 'megablast' > GRCH37_blastn_31mers_mega.out blastn -query unique_31mers.fa -db Homo_sapiens.GRCh37.dna.primary_assembly -task 'blastn' -outfmt "6 delim=\t" > GRCH37_blastn_31mers.out
For context, the 31mers come from viral sequences.