esteinig
commented
7 months ago Hello! At the moment the thresholds are hard-coded, although that could probably be changed, as they are pretty arbitrary. I'll flag it for the next release as a feature, thanks for letting me know this is of interest.
In the meantime, you can work around it using nanoq, awk and bash - quite verbose, but it should work:
# output read q values as txt file and get total reads from summary stats
total_reads=$(nanoq -i test.fq -s -Q qual.txt | cut -d' ' -f1)
# count reads greater than threshold in list
gt9=$(awk '$1>9{c++} END{print c+0}' qual.txt) # > 9.0
gt8=$(awk '$1>8{c++} END{print c+0}' qual.txt) # > 8.0
# divide and multiply for percentage
echo "scale=2 ; ($gt9 / $total_reads)*100" | bc # > 9.0
echo "scale=2 ; ($gt8 / $total_reads)*100" | bc # > 8.0
dear developer
after using -vvv in the command line I am getting the below results
Read quality thresholds (Q)
I am wondering if is it possible to get the percentage of reads with >8 or >9 too?
THanks