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189 results • Page
1 of 4
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Filtering for tag:
taxonomy
•
reset
0
votes
0
replies
74
views
Taxonomic Bar Plots for too many values
programming
G
taxonomy
P
gene
18 days ago by
saraswati.awasthi22
• 0
0
votes
1
reply
94
views
Edit the NCBI Taxonomy with ete3 toolkit ?
taxonomy
taxdump
ncbi
ete3
toolkit
26 days ago by
Pierre
• 0
1
vote
4
replies
187
views
Command line Taxa search within SRA / NCBI Trace
SRA
Taxa
Taxonomic
taxonomy
4 weeks ago by
poppersrules
• 0
1
vote
1
reply
152
views
blastx diamond returns taxid "NA" for some sequence queries
blastx
diamond
taxonomy
7 weeks ago by
pedrorodrigues
▴ 10
0
votes
1
reply
133
views
Counting the number of species from NCBI Taxonomy browser
Taxonomy
NCBI
updated 8 weeks ago by
shenwei356
5.8k • written 8 weeks ago by
adarshpp1997
• 0
0
votes
1
reply
162
views
How to identify lineages from whole genome assemblies
genome
Assembly
taxonomy
3 months ago by
ddh8602
• 0
0
votes
1
reply
1.6k
views
Tutorial:
Getting the lineage of an organism from NCBI taxonomy data
taxonomy
python
biosql
Tutorial
updated 4 months ago by
biofysikos
• 0 • written 2.7 years ago by
Vimal Kumar Velayudhan
▴ 200
0
votes
3
replies
1.3k
views
Is it possible to get taxonomy identifiers from diamond output without using --taxonmap during makedb?
diamond
blast
protein
alignment
taxonomy
updated 6 months ago by
Sej Modha
4.8k • written 16 months ago by
O.rka
▴ 290
0
votes
1
reply
188
views
In NCBI names.dmp file what does it mean to have multiple nodes pointing to different names?
NCBI
names.dmp
nodes.dmp
taxonomy
6 months ago by
psun
• 0
1
vote
4
replies
304
views
unclassified taxonomy rank
16s
taxonomy
updated 6 months ago by
Mensur Dlakic
★ 10k • written 6 months ago by
mrashad
▴ 50
1
vote
5
replies
283
views
MaarjAM database download related problems
maarjam
database
fungi
taxa
taxonomy
updated 7 months ago by
405329753
• 0 • written 7 months ago by
the_dummy
▴ 30
1
vote
1
reply
390
views
Taxonomic classification of MAGs
metagenomics
genome
taxonomy
binning
updated 7 months ago by
Mensur Dlakic
★ 10k • written 7 months ago by
c.e.chong
▴ 40
0
votes
0
replies
212
views
Kraken taxonomy sublevels
kraken
taxonom
kraken
taxonomy
8 months ago by
fyfes
▴ 30
6
votes
6
replies
390
views
How to determine contig taxonomy from metagenome?
contig
taxonomy
metagenome
identity
updated 8 months ago by
lagartija
▴ 90 • written 8 months ago by
Audrey
▴ 50
0
votes
1
reply
2.0k
views
How to get pfam seed sequence taxonomy info?
pfam
ncbi
blast
taxonomy
updated 8 months ago by
jubillante
• 0 • written 5.8 years ago by
beegrackle
▴ 90
1
vote
2
replies
2.2k
views
Tutorial:
How to get full taxonomy classification using taxize and myTAI
taxonomy
tool
R
Tutorial
updated 8 months ago by
wangdepin5135
• 0 • written 3.0 years ago by
Daniel
★ 3.8k
2
votes
4
replies
381
views
Fasta Taxonomy Annotation
fasta
annotation
taxonomy
updated 8 months ago by
h.mon
32k • written 9 months ago by
zach
▴ 10
3
votes
4
replies
373
views
Tool:
kraken2table, an analogous to kaiju2table
kraken
kaiju
taxonomy
classification
Tool
8 months ago by
Macspider
★ 3.4k
6
votes
5
replies
755
views
converting taxID to taxonomy
NCBI
TAXONOMY
TAXID
terminal
updated 10 months ago by
SilentGene
▴ 50 • written 13 months ago by
Freddy
▴ 30
6
votes
11
replies
276
views
biopython entrez lost connection?
python
biopython
ncbi
taxonomy
10 months ago by
flogin
▴ 250
0
votes
2
replies
395
views
Extract 16S rRNA V6 region
16S rRNA
MOTHUR
taxonomy
microbiome
12 months ago by
dpc
▴ 170
0
votes
8
replies
444
views
Conversion of fasta file to taxon id(?)
sequence
BLAST
taxon id
Ncbi
Taxonomy
12 months ago by
sajjalwaqas
• 0
7
votes
11
replies
352
views
how to find the kingdom for a taxon id using the terminal?
ncbi
taxonomy
kingdom
terminal
updated 13 months ago by
GenoMax
99k • written 13 months ago by
Freddy
▴ 30
1
vote
3
replies
209
views
small representative database
taxonomy
data
genomes
proteomes
updated 13 months ago by
Mensur Dlakic
★ 10k • written 13 months ago by
lagartija
▴ 90
1
vote
3
replies
375
views
Using Entrez to find the taxonomy for an accession number
accession_number
taxonomy
NCBI
entrez
updated 14 months ago by
vkkodali
★ 2.5k • written 14 months ago by
Freddy
▴ 30
7
votes
5
replies
1.3k
views
How to get Taxonomy and Taxon ID for an Accession number using R/Python?
R
PYTHON
accession numer
taxonomy
updated 14 months ago by
Chirag Parsania
★ 1.9k • written 14 months ago by
Freddy
▴ 30
0
votes
1
reply
465
views
Kraken_results or Kraken_report? Which file to consider ?
kraken
taxonomy
pathways
updated 14 months ago by
onestop_data
▴ 280 • written 16 months ago by
data_diva
• 0
0
votes
0
replies
319
views
Taxonomy from Pfam database
pfam
taxonomy
bioinformatics
16 months ago by
shibl_a
▴ 20
1
vote
1
reply
487
views
taxonomic classification with rna-seq data
taxonomy
rnaseq
Kraken
kaiju
IMSA+A
16 months ago by
vm.higareda
▴ 20
2
votes
1
reply
1.8k
views
Tree file and taxonomy
tree
taxonomy
mothur
updated 16 months ago by
Biostar
20 • written 4.6 years ago by
yuki.weber81
▴ 10
0
votes
5
replies
554
views
Taxonomic assignment of bins found by Maxbin2
Maxbin2
bins
taxonomy
updated 17 months ago by
Mensur Dlakic
★ 10k • written 17 months ago by
Hansen_869
▴ 20
2
votes
9
replies
371
views
how many genomes from BLAST hit should be considered for phylogeny tree analysis?
phylogeny
tree
taxonomy
genome
updated 17 months ago by
Biostar
20 • written 18 months ago by
DanielC
▴ 140
1
vote
2
replies
940
views
Database Recommendations for 16S-seq of the V4 Region
16S-seq
Taxonomy
SILVA
microbiome
DADA2
18 months ago by
dmj6ab
▴ 10
1
vote
2
replies
300
views
What is the difference between "root" and "cellular organisms" in NCBI taxonomy?
taxonomy
classification
updated 18 months ago by
Pierre Lindenbaum
135k • written 18 months ago by
luise.schulte
• 0
3
votes
3
replies
576
views
Missing GenBank identifier to NCBI taxonomy mapping
ncbi
taxonomy
genbank
updated 18 months ago by
h.mon
32k • written 18 months ago by
martinsteinegger
▴ 30
2
votes
0
replies
329
views
Tool:
PipeTaxon: A tool to exposes the NCBI taxonomy database as a REST API.
taxonomy
ncbi
python
Tool
18 months ago by
commonsnook
▴ 40
9
votes
10
replies
8.6k
views
Download whole dataset from NCBI Taxonomy
NCBI
Taxonomy
updated 19 months ago by
sebastian.zn
• 0 • written 5.4 years ago by
stackf03
▴ 30
4
votes
4
replies
1.2k
views
Mapping NCBI Genome Accessions - NCBI Taxonomy IDs
genome
taxonomy
GenBank
NCBI
updated 20 months ago by
GenoMax
99k • written 20 months ago by
mar.ark.parr
▴ 40
2
votes
3
replies
355
views
Interproscan sequence classification
interproscan
taxonomy
taxonomic classification
22 months ago by
drikaul
▴ 20
8
votes
17
replies
3.0k
views
Extract Tree Topology From Ncbi Taxonomy Database
bioperl
taxonomy
updated 23 months ago by
peterlageweg603
▴ 10 • written 8.4 years ago by
Lhl
▴ 730
0
votes
1
reply
273
views
find bacteria lifestyle
bacteria
taxonomy
lifestyle
23 months ago by
Xylanaser
▴ 60
4
votes
1
reply
483
views
How to identify best-hit taxonomy of many gene sequences efficently
sequence
gene
taxonomy
ncbi
23 months ago by
gwrathe
• 0
3
votes
2
replies
490
views
Taxids from BLAST search that are not present in names.dmp or nodes.dmp
blast
taxonomy
23 months ago by
salanova.elliott
• 0
1
vote
6
replies
509
views
taxonomic identification least common ancestor approach
phylogeny
taxonomy
phylum
genus
updated 23 months ago by
Asaf
8.6k • written 23 months ago by
Moses
▴ 120
3
votes
4
replies
427
views
Microbiome Taxonomy composition
microbiome
taxonomy
updated 23 months ago by
Carambakaracho
★ 2.4k • written 23 months ago by
genomics Newbie
▴ 60
1
vote
2
replies
519
views
How to get 'nucl_est.assession2taxid .gz' from NCBI
NCBI
Taxonomy
updated 23 months ago by
GenoMax
99k • written 23 months ago by
taylor
• 0
1
vote
3
replies
568
views
Complete phylogenetic trees?
taxonomy
phylogenetic
tree
tree of life
2.1 years ago by
gtrwst9
• 0
2
votes
4
replies
573
views
Filter human parasites from taxonomic profiling with Kraken
parasites
metagenomics
taxonomy
updated 2.1 years ago by
ctseto
▴ 280 • written 2.1 years ago by
Fungsten
• 0
3
votes
3
replies
4.1k
views
Filter command-line BLAST results by organism
blast
alignment
genome
taxonomy
updated 2.1 years ago by
Biostar
20 • written 6.5 years ago by
jdromano2
▴ 10
4
votes
8
replies
4.0k
views
Relative abundance fro metagenomics samples
metagenomics
bwa
taxonomy
relative abundance
updated 2.1 years ago by
lagartija
▴ 90 • written 4.2 years ago by
David
▴ 200
189 results • Page
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Recent Votes
Comment: Keep values from VCF file into Ensembl VEP annotation
Answer: Creating reference genome for mapping and then selecting
Comment: Creating reference genome for mapping and then selecting
Answer: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
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Comment: Keep values from VCF file into Ensembl VEP annotation
by
dare_devil
★ 1.4k
it would be great and helpful to others if you share your answer here.
Answer: Expression of gene of interest across conditions in single-cell data
by
jared.andrews07
9.1k
Take a look at [dittoSeq](http://www.bioconductor.org/packages/release/bioc/vignettes/dittoSeq/inst/doc/dittoSeq.html) for viz options - it…
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by
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9.1k
You need pre-defined variants for Vartrix. Typically it's used in conjuction with WGS/WES from bulk tissue to look for clonal variants in d…
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by
paria.alipour
▴ 20
Oh, I'm sorry. I already posted it in here the https://www.biostars.org/p/457243/#9464486. I've added the images
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
by
Quanyou
• 0
This seems OK when one gene generates only one transcirpt. But when one gene has multiple transcripts, these code would return a table wher…
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
by
Quanyou
• 0
This seems feasible. But I want to convert tens of thousands of transcript IDs. Could you tell me how can I make it through sequene search?
Answer: bbmap, mapq and uniquelly mapped reads filtering
by
GenoMax
99k
Many threads exist that show how to extract uniquely mapped reads. Here are a couple of examples:<br> https://www.biostars.org/p/276216/#27…
Comment: Cell composition in each condition of single cell data
by
rpolicastro
5.1k
The images seem to be missing from your post
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by
kra277
• 0
Thank you very much for this. Much appreciated.
Comment: Limma experiment design and making contrasts
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Hi, these follow the same principles as formulae used in regression modelling, so, you may want to focus on that (when searching). What lim…
Comment: Limma experiment design and making contrasts
by
kra277
• 0
That is very insightful. Thank you very much for the answer. Also, if I may ask, could you please point me to the articles for understandin…
Comment: Keep values from VCF file into Ensembl VEP annotation
by
brunobsouzaa
▴ 520
Thanks Man... I've wroten a simple awk command for this task! Everything is working fine.
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Do you have exact command used by the author? I guess that not all details was presented in the paper. You can always ask the corresponding…
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Your github page appears to live here now https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/gxf.md
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Istvan Albert
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I am not all that knowledgeable of Cytoscapes features and scripting capabilities, but if it does not support that operation you can expo…
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