search

DaehwanKimLab / centrifuge

Classifier for metagenomic sequences
GNU General Public License v3.0
246 stars 73 forks source link

--out-fmt option #87

Closed wyim-pgl closed 6 years ago

wyim-pgl commented 6 years ago

Hello folks,

I have a simple question regarding --out-fmt options. The default --out-fmt tab will not work with --un, --al, --al-con & etcs, I need to set it to sam for decontamination. Since "pavian" provides a fancy graph, I need to use --out-fmt tab as well as centrifuge-kreport. The problem is that I set --out-fmt option to tab, I cannot get the unmapped or mapped reads.

How can I get the output for unmapped or mapped reads and input for centrifuge-kreport at once ? Currently my resolution is "running twice" with tab and sam.

Cheers,

Won

mourisl commented 6 years ago

I've upload a new version of kreport and it should handle your case.