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DaehwanKimLab / centrifuge

Classifier for metagenomic sequences
GNU General Public License v3.0
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centrifuge-kreport values do not ad #276

Open pablorr24 opened 1 month ago

pablorr24 commented 1 month ago

Hi, I've been working on Centrifuge, and using the centrifuge-kreport tool to convert my results to kraken2 format. I'm using:

centrifuge-kreport -x /.../database/db_prefix centrif_report.tsv > kreport.txt

I am getting a kraken report but the values seem to differ. In the screenshot the Centrifuge report (above) values for Bacillus differ from those on the kraken report (below). I'm not sure if I'm interpreting something incorrectly, or there might be an issue with the code.

image

Best regards, Pablo R

mourisl commented 1 month ago

Indeed, the 5 reads marked in the numUniqueReads should be reflected in the report. I'll check whether I can reproduce this issue on our data or ERR3077553. Thank you for reporting it!