Kraken taxonomy sublevels

Hi, Could you please tell me what does Kraken taxonomy sublevel mean? My output in taxonomy column is sometimes P (phylum) or sometimes P1 or P2. Thank you

kraken taxonom kraken taxonomy

• 1,235 views • link

written 6.0 years ago by fyfes •

0 answers

No answers yet.

More posts like this

miRNA annotation miRge3.0
written 2.7 years ago by bas2020 •

Hi everybody, I aligned murine miRNA using miRge3.0. However, somehow the nomenclature/annotation seems to be odd. I could not find any rules for it online. …
kraken on nt library
written 3.2 years ago by Francois Piumi •

Hi, I'd like to perform a kraken library on the nt library, since my fastq sequences are not human I build a kraken nt library, …
Bowtie2 and subprocess issue
written 4.0 years ago by robjohn70000

Hi, I tried running bowtie2 in python using subprocess without any success. Codes: REFGENOME='/path-to-genome/genome.fasta' P1='/path-to-fastq/P1.fastq.bz2' P2='/path-to-fastq/P2.fastq.bz2' cmd=['bowtie2','--quiet','-p','10','--dovetail','--no-head','--no-sq','-x',REFGENOME,'-1',P1,'-2',P2,'-S', 'out.sam'] subprocess.Popen(cmd, shell=True) Error: No index, query, or …
Help using Kraken - chimera filtering
written 4.4 years ago by SushiRoll •

Hi everyone, I am using Kraken on a set of Illumina reads from a metagenomics project. In the past I have used dada2 for 16S …
Arranging two plots in ggplot
written 4.6 years ago by Space_Life •

Hi, I have a quick question. I made two plots p1 and p2 and arranged them in two rows (p1 at top, p2 at bottom) …
From accession ID to phylum taxid
written 5.8 years ago by doinelpierrot •

Hello guys, I have a list of 10 000 accessions id from blast in a txt file (XP_002184977.1 GBG35237.1) and I would like to have …
Relative abundance in phyloseq and biplot
written 6.3 years ago by Bioinfonext

Hi, I do have relative abundance in phyloseq object, could you please let me know how I can plot biplot with taxonomy at phylum level …
how to arrange multiple TOMplot() and plotDendroAndColors() in one page
written 6.5 years ago by kingwind333 •

In WGCNA, I got several TOM and dendroandcolor plots via the TOMplot() and plotDendroAndColors(). I want to arrange them in one page in a pdf …
Relatedness vs relatedness2 from vcftools give different results
written 8.5 years ago by Sharon

Hello All **How to you think about this relatedness results?** When I use relatedness2 in vcftools I got this: vcftools --gzvcf p123.vcf.gz --relatedness2 INDV1 INDV2 …
Compare two matrix
written 9.2 years ago by Amy •

I have two matrix. The first one is a **genotype matrix** in which: - Rows represent locus - Columns represent samples - Each value represents …