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What are TaxReads for Root? #188

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peradastra opened this issue Oct 10, 2024 · 0 comments
Open

What are TaxReads for Root? #188

peradastra opened this issue Oct 10, 2024 · 0 comments

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@peradastra
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Dear all,

Can someone please explain what would cause reads to be assigned to taxReads for no rank root?
Are they reads which can be classified but just not uniquely?
See the 57 reads in the KrakenUniq report bellow.

KrakenUniq Report

%	reads	taxReads	kmers	dup	cov	taxID	rank	taxName
0.06999	16	16	101539	1.06	0.0007595	0	no rank	unclassified
99.93	22844	57	4085491	1.22	8.56e-05	1	no rank	root
99.19	22675	0	4038991	1.22	8.526e-05	131567	no rank	  cellular organisms
...

Here's what these reads look like...

C       M03901:710:000000000-LM4VW:1:2108:18162:5574    1       302     1:120 A:31 1:121
C       M03901:710:000000000-LM4VW:1:1109:26723:17965   1       301     1:121 A:31 1:119
C       M03901:710:000000000-LM4VW:1:1110:10566:6434    1       267     1:103 A:31 1:103
C       M03901:710:000000000-LM4VW:1:1110:29104:15907   1       302     1:121 A:31 1:120
C       M03901:710:000000000-LM4VW:1:1111:19257:7058    1       141     1:40 A:31 1:40
C       M03901:710:000000000-LM4VW:1:1111:5749:10830    1       204     1:104 A:31 1:39
C       M03901:710:000000000-LM4VW:1:1111:12731:13558   1       107     1:23 A:31 1:23

I'm trying to build a pipeline and need all reads to sum to the number of input reads.
Not sure how to categorize these reads as they don't go into any domain but are not unclassified.

Best,
Per

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