Hey, quick question. I need the final number of re...
# taxprofilerh
Håkon Kaspersen
09/09/2026, 11:09 AMHey, quick question. I need the final number of reads of the analysis ready fastqs, although I did not output the reads themselves, so I can't verify this. Is this the same as the "reads_unmapped" column in the multiqc_samtools_stats.txt file in the output?
j
James Fellows Yates
09/09/2026, 4:00 PMActuaylly no, that's not supported at the moment... although it would make sense to support it!
James Fellows Yates
09/09/2026, 4:00 PMIf you could make an issue, I _think_I could add it quite quickly
James Fellows Yates
09/09/2026, 4:01 PMYou can't use the bbduk or samtools bits as these both happen before run merging... so if you do run-merging it could be misleading
James Fellows Yates
09/09/2026, 4:01 PMIf you can send your command I can tell you roughly where that info may apply
James Fellows Yates
09/09/2026, 4:02 PMIf you are running host-removal, then yeah probably the
samtools stats unmappedJames Fellows Yates
09/09/2026, 4:02 PMBut it would be useful to have the actual numbers in the analysis ready fastqs regardless what you are running for preprocessing (e.g. wiht
seqkith
Håkon Kaspersen
09/14/2026, 7:21 AMThanks for your reply, James! I have added an issue on this. For this run, I did not have runmerging activated, as I only had one run for each sample (which is usually the case for us).
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