Hello, I am running kneaddata (v0.10.0) through biobakery workflows on paired reads, but I have not been able to find a description of how to interpret the read_count_table output.
Below are the counts for R1:
|decontaminated hg37dec_v0.1 pair1|10060306|
|decontaminated hg37dec_v0.1 orphan1|744693|
And here for R2:
|decontaminated hg37dec_v0.1 pair2|10060306|
|decontaminated hg37dec_v0.1 orphan2|1246013|
- What does each of these numbers mean? I have some guesses, but would love an “official” description.
- How should I calculate the % human reads removed?
- Are there any default qc thresholds in kneaddata/biobakery, or any suggested ones?
Thank you in advance!