extract_kraken_reads.py accept bracken reports?

[Sabrin2020]

Hi Team,

Could extract_kraken_reads.py accept bracken reports too?
As I have up to 40% of reads as unclassified by kraken, I do not not want to loose info in those unclassified reads in downstram analysis.

Could then using bracken outputs help here?

Best Regards,
Sabrin

[heccup]

hello ,i have the same question,can we conmunicate forther

[Jonchk1104]

Hello everyone.
I have the same question about problem using the extract_kraken_reads.py command for Bracken reports.
Will it be possible to create a new output file after running the Bracken, so we can use the new output file used for running extract_kraken_reads.py?