Open beryl-au opened 1 month ago
Not in the output file, but they will appear in the bwa output (which you can direct with --tmp-prefix
, but it will still be removed at the end of the run I think). You could just run bwa yourself with bwa mem -v 1 -k 8 ref.fa kmers.fa
Thanks for your reply, if we use the annotation results( annotated_kmers.txt) of annotate_hits_pyseer directly for analysis, is there a mapping quality for such k-mer annotations?
I think these are omitted in the output file sorry. @mgalardini does your new pipeline help with this at all?
No unfortunately, we are mapping k-mers back using a similar approach. @beryl-au, could you expand a bit on what you would like the mapping quality for? it could be interesting to implement
Possibly similar to some of the literature restricting the analysis to reads with a minimum mapping quality of 10 or 20 to determine confident mappings?
Sure, that seems like an interesting use case, although usually you would be mapping unitigs back to the same genomes it came from, and so I expect most (?) mappings to be exact matches. Worth looking into eventually though
Hi, We have run annotate_hits_pyseer to annotate k-mers.,but we are not sure if it has mapping quality when annotating k-mers? Do you have any suggestions? Thank you in advance!