Hi Ben,
I was playing around with the new bowtie version, and I noticed that specifying the --best flag resulted in an output that had a different number of mappings than when the flag is omitted. However, in the bowtie documentation, it says that --best does not change which alignments are considered valid. I tried this with multiple sets of reads, and each time the number of alignments differed. Is this a bug or am I misunderstanding the effects of --best? The other flags I was using (in both cases) were -S, -p, --solexa1.3-quals, --al, and --un.
Thanks!
I was playing around with the new bowtie version, and I noticed that specifying the --best flag resulted in an output that had a different number of mappings than when the flag is omitted. However, in the bowtie documentation, it says that --best does not change which alignments are considered valid. I tried this with multiple sets of reads, and each time the number of alignments differed. Is this a bug or am I misunderstanding the effects of --best? The other flags I was using (in both cases) were -S, -p, --solexa1.3-quals, --al, and --un.
Thanks!
Comment