Maybe there is already a way to extract this information, but is it possible to add th

Can you clarify? For example, this is the output I get: <div cla

add unmatched reads to report table about centrifuge HOT 3 CLOSED

daehwankimlab commented on July 17, 2024

add unmatched reads to report table

from centrifuge.

Comments (3)

mourisl commented on July 17, 2024

Sorry for this late reply. This information can be obtained from the read classification output.

from centrifuge.

igordot commented on July 17, 2024

Can you clarify?

For example, this is the output I get:

name,taxID,taxRank,numReads,numUniqueReads
Leucoraja erinacea,7782,species,12680,11792
Mus musculus,10090,species,12553,3532
Danio rerio,7955,species,7686,2782
Cyprinus carpio,7962,species,6727,2669
Homo sapiens,9606,species,7607,2034
Vigna angularis var. angularis,157739,varietas,3267,1733
Ovis canadensis canadensis,112262,subspecies,3052,1412
Bathyraja eatonii,298348,species,1637,1060
Raja eglanteria,33514,species,1110,962
Apteryx australis mantelli,202946,subspecies,1738,817
Chryseobacterium sp. StRB126,878220,species,1062,700
Solanum pennellii,28526,species,1514,651
Oryzias latipes,8090,species,1544,620
Vitis vinifera,29760,species,1168,450
Solanum lycopersicum,4081,species,1492,423
Echinostoma caproni,27848,species,1049,421
Protopolystoma xenopodis,117903,species,831,362
Salmo salar,8030,species,918,362
Callorhinchus milii,7868,species,929,355
Trichobilharzia regenti,157069,species,791,339

I only see matches.

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mourisl commented on July 17, 2024

Yes, the report file is for matched information. In the raw output of Centrifuge, where it has one ( or several lines ) for each read, you can count the reads with the taxonomy rank "unclassified".

from centrifuge.

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