ReadCount vs ReadCountAln

[Former user]

Hi Philip

If I look at the *.mapstat file, there are mostly less aligned reads (ReadCountAln) than mapped reads (ReadCount). However, I can't find on what basis some mapped reads are not considered for alignment?

I used the following command:

kma -i "Zymo-GridION-EVEN-BB-SN-PCR-R10HC-flipflop.fq" -o "kma_files/output" -t_db /db/gene_detection/ResFinder/kma/resfinder-clustered_80 -t 24 -1t1 -ef -a -mrs 0.0 -bcNano -bc 0.7 -tmp /scratch/ -matrix -verbose 

[ptlcc]

Hi,

Most mapped reads are considered for alignment, with your setting s all is. But some reads may be unable to align with a high enough score to be accepted, while it is possible to map them (ie. determine their likely origin given the database).

Best,
Philip