Identify total number of reads after host-removal not just %
Closed this issue · 1 comments
Joon-Klaps commented
Description of feature
Total input reads after preprocessing (final step host removal) just reports a percentage but not a number. This should be a number. Because mqc doesn't annotate the kraken output, use a try and search for the following
Consider checking for
Sample Bacteria Eukaryota Archaea Other Unclassified
LVE00136 63238.0 88.0 16.0 25.0 7798362.0
...Here Bacteria or Eukaryota can be present but just not Viruses . Then the final column can be extracted.
Joon-Klaps commented
No need as fastqc is ran after host deduplication