How to extract Unclassified reads from input

[shameem356]

Ask away!

I ran the pipeline with the minimap2 classifier, and the results show that out of 500,000 reads, 70,000 reads are classified as Unclassified or Unknown. I would like to know how I can extract these unknown reads from the input FASTQ files.

[nggvs]

Hi @shameem356 ,
thanks for using the workflow! This is planned for a future release. Meanwhile you can take a look on how to extract the Unclassified reads in the blogpost: https://labs.epi2me.io/post-meta-analysis/#how-to-recover-unmapped-reads-from-bam-files
Thank you very much in advance!