About how to track cov19

[juychen]

Hi,

In your paper, I saw that you have analysis on virus.
But this part is missing in the tutorial to run virus detection?
Are there any option that we can switch to call virus?

Regards,
Junyi

[ncrna]

Thank you for your interest in using PathogenTrack! PathogenTrack will detect bacteria, virus, and fungi in default mode, and in the output matrix, each row represents a microbe species, you can track virus by the row names. Hope it would help!

Wei Zhang

[juychen]

Hi, I would like to know how to interpret the report.
What are the numbers in each of the columns?
For example, 442374 is the number of reads or UMI counts?

89.06 442374 442374 U 0 unclassified
10.94 54356 745 R 1 root
10.79 53601 3766 R1 131567 cellular organisms
10.03 49833 0 D 2759 Eukaryota
10.03 49833 0 D1 33154 Opisthokonta
10.03 49833 0 K 33208 Metazoa
10.03 49833 0 K1 6072 Eumetazoa
10.03 49833 0 K2 33213 Bilateria
10.03 49833 0 K3 33511 Deuterostomia
10.03 49833 0 P 7711 Chordata
10.03 49833 0 P1 89593 Craniata
10.03 49833 0 P2 7742 Vertebrata
10.03 49833 0 P3 7776 Gnathostomata
10.03 49833 0 P4 117570 Teleostomi
10.03 49833 0 P5 117571 Euteleostomi
10.03 49833 0 P6 8287 Sarcopterygii
10.03 49833 0 P7 1338369 Dipnotetrapodomorpha
10.03 49833 0 P8 32523 Tetrapoda
10.03 49833 0 P9 32524 Amniota
10.03 49833 0 C 40674 Mammalia
10.03 49833 0 C1 32525 Theria
10.03 49833 0 C2 9347 Eutheria
10.03 49833 0 C3 1437010 Boreoeutheria
10.03 49833 0 C4 314146 Euarchontoglires
10.03 49833 0 O 9443 Primates
10.03 49833 0 O1 376913 Haplorrhini
10.03 49833 0 O2 314293 Simiiformes
10.03 49833 0 O3 9526 Catarrhini
10.03 49833 0 O4 314295 Hominoidea
10.03 49833 0 F 9604 Hominidae
10.03 49833 0 F1 207598 Homininae
10.03 49833 0 G 9605 Homo
10.03 49833 49833 S 9606 Homo sapiens

[ncrna]

From the attached report, "442374" is the number of reads that classified by kraken2. In the final step, PathogenTrack will deduplicate the reads into UMI counts. Hope it would help!