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comments
2
votes
1
reply
439
views
Tool:
Just released VEBA 2.0 in Nucleic Acids Research, a modular genome-resolved metagenomics/metatranscriptomics software suite that can handle prokaryot…
metatranscriptomics
metagenomics
microbiome
veba
9 weeks ago by
O.rka
▴ 740
0
votes
0
replies
226
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
3 months ago by
O.rka
▴ 740
0
votes
0
replies
232
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
4 months ago by
O.rka
▴ 740
0
votes
1
reply
583
views
Comment:
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
4 months ago by
O.rka
▴ 740
1
vote
3
replies
583
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 4 months ago by
Mensur Dlakic
★ 28k • written 4 months ago by
O.rka
▴ 740
0
votes
0
replies
442
views
Comment:
Comment: Help with understanding the identifier mapping tables in the backend of HUMAnN
4 months ago by
O.rka
▴ 740
0
votes
2
replies
442
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
4 months ago by
O.rka
▴ 740
0
votes
0
replies
487
views
Comment:
Comment: Why are gene models from JGI non-sense when using AGAT to to extract proteins?
5 months ago by
O.rka
▴ 740
0
votes
2
replies
487
views
Why are gene models from JGI non-sense when using AGAT to to extract proteins?
translation
models
gif
gene
cgi
5 months ago by
O.rka
▴ 740
1
vote
1
reply
650
views
How to estimate -g genome-size for Flye for de novo genome or for --meta mode when using Metaflye?
assembly
fasta
genomics
nanopore
pacbio
updated 6 months ago by
akshay
▴ 10 • written 9 months ago by
O.rka
▴ 740
0
votes
1
reply
649
views
How can I calculate the percent of bases covered in the query assembly relative to the reference assembly?
samtools
updated 7 months ago by
dthorbur
★ 2.4k • written 7 months ago by
O.rka
▴ 740
0
votes
0
replies
857
views
Comment:
Comment: How to use Nextflow to call scripts from different environments?
8 months ago by
O.rka
▴ 740
1
vote
2
replies
857
views
How to use Nextflow to call scripts from different environments?
anaconda
conda
nextflow
8 months ago by
O.rka
▴ 740
2
votes
1
reply
663
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam
sam
reads
fastq
updated 9 months ago by
rpolicastro
13k • written 9 months ago by
O.rka
▴ 740
2
votes
3
replies
896
views
How to check if my sequence is DNA or Protein in BioPython?
genomics
biopython
fasta
updated 9 months ago by
Joe
21k • written 9 months ago by
O.rka
▴ 740
1
vote
1
reply
710
views
How to download taxonomy/lineage/taxonid information for JGI genome organism codes? (e.g., MycoCosm and PhycoCosm)
jgi
genomics
phycocosm
mycocosm
taxonomy
10 months ago by
O.rka
▴ 740
1
vote
0
replies
710
views
Answer:
Answer: How to download taxonomy/lineage/taxonid information for JGI genome organism co
10 months ago by
O.rka
▴ 740
0
votes
0
replies
687
views
Comment:
Comment: Why are some HUMAnN features in [name]_pathabundance.tsv missing taxonomy?
10 months ago by
O.rka
▴ 740
0
votes
2
replies
687
views
Why are some HUMAnN features in [name]_pathabundance.tsv missing taxonomy?
metagenomics
metabolism
humann
biobakery
metatranscriptomics
10 months ago by
O.rka
▴ 740
0
votes
1
reply
579
views
How to download genomes and proteins from JGI in bulk via the command line?
jgi
cli
updated 11 months ago by
Ram
44k • written 11 months ago by
O.rka
▴ 740
1
vote
3
replies
826
views
How to convert between UniRef50 to EC/enzyme number?
Uniref
conversion
uniprot
enzyme
updated 11 months ago by
Elisabeth Gasteiger
★ 2.4k • written 11 months ago by
O.rka
▴ 740
0
votes
0
replies
826
views
Comment:
Comment: How to convert between UniRef50 to EC/enzyme number?
11 months ago by
O.rka
▴ 740
0
votes
0
replies
859
views
Comment:
Comment: How to run TRUST4 for BCR/TCR detection using 10X data?
11 months ago by
O.rka
▴ 740
0
votes
2
replies
859
views
How to run TRUST4 for BCR/TCR detection using 10X data?
immunology
trust4
illumina
10x
11 months ago by
O.rka
▴ 740
7
votes
9
replies
2.1k
views
6 follow
How can I transfer gene models to a new assembly?
gene
Assembly
updated 12 months ago by
Philipp Bayer
8.7k • written 4.4 years ago by
O.rka
▴ 740
0
votes
1
reply
963
views
Comment:
Comment: When counting ASVs in DADA2, does a hit/count only occur at 100% alignment perce
12 months ago by
O.rka
▴ 740
0
votes
1
reply
2.1k
views
Answer:
Answer: How can I transfer gene models to a new assembly?
12 months ago by
O.rka
▴ 740
3
votes
3
replies
963
views
When counting ASVs in DADA2, does a hit/count only occur at 100% alignment percent identity?
metagenomics
qiime2
amplicon
16s
dada2
updated 12 months ago by
andres.firrincieli
3.7k • written 12 months ago by
O.rka
▴ 740
0
votes
0
replies
408
views
What criteria are used to determine significant HMMER hits?
kegg
protein
kofamscan
annotation
metagenomics
13 months ago by
O.rka
▴ 740
0
votes
1
reply
715
views
Using tRNAscan-SE for mitochondria tRNA from microeukaryotes like protists and yeast?
trnascan
yeasts
eukaryotes
protists
trna
updated 14 months ago by
shelkmike
★ 1.3k • written 14 months ago by
O.rka
▴ 740
3
votes
2
replies
2.4k
views
Help speeding up HMMER's HMMSearch algorithm for large fasta file with GNU Parallel
protein
parallel
hmmer
hmm
bash
updated 14 months ago by
lieven.sterck
15k • written 3.1 years ago by
O.rka
▴ 740
0
votes
1
reply
2.0k
views
Comment:
Comment: How can I speed up wget from UniProt for UniRef90/50 fasta?
15 months ago by
O.rka
▴ 740
0
votes
1
reply
2.0k
views
Comment:
Comment: How can I speed up wget from UniProt for UniRef90/50 fasta?
15 months ago by
O.rka
▴ 740
0
votes
1
reply
2.0k
views
Comment:
Comment: How can I speed up wget from UniProt for UniRef90/50 fasta?
15 months ago by
O.rka
▴ 740
0
votes
7
replies
2.0k
views
How can I speed up wget from UniProt for UniRef90/50 fasta?
wget
download
uniprot
uniref
updated 15 months ago by
Mensur Dlakic
★ 28k • written 15 months ago by
O.rka
▴ 740
0
votes
0
replies
25k
views
Comment:
Comment: Variant call format (VCF) file, how to get statistics per sample?
16 months ago by
O.rka
▴ 740
0
votes
0
replies
1.4k
views
Comment:
Comment: Should you specify "-p" for paired end reads using featureCounts?
16 months ago by
O.rka
▴ 740
0
votes
1
reply
1.4k
views
Comment:
Comment: Should you specify "-p" for paired end reads using featureCounts?
16 months ago by
O.rka
▴ 740
4
votes
6
replies
1.4k
views
Should you specify "-p" for paired end reads using featureCounts?
fastq
rnaseq
genomics
16 months ago by
O.rka
▴ 740
0
votes
0
replies
344
views
How can I get taxa relative abundances from HUMAnN?
metagenomics
humann
biobakery
metatranscriptomics
16 months ago by
O.rka
▴ 740
0
votes
0
replies
2.6k
views
Comment:
Comment: Most efficient way to run Diamond against a very very large database (i.e., NCBI
17 months ago by
O.rka
▴ 740
0
votes
1
reply
2.6k
views
Comment:
Comment: Most efficient way to run Diamond against a very very large database (i.e., NCBI
17 months ago by
O.rka
▴ 740
5
votes
9
replies
2.6k
views
6 follow
Most efficient way to run Diamond against a very very large database (i.e., NCBI's NR)?
protein
annotation
alignment
diamond
nr
updated 12 months ago by
GenoMax
145k • written 17 months ago by
O.rka
▴ 740
0
votes
1
reply
1.0k
views
Comment:
Comment: How can I determine the number of detected genes and detected transcripts/isofor
17 months ago by
O.rka
▴ 740
0
votes
1
reply
1.0k
views
Comment:
Comment: How can I determine the number of detected genes and detected transcripts/isofor
17 months ago by
O.rka
▴ 740
0
votes
5
replies
1.0k
views
How can I determine the number of detected genes and detected transcripts/isoforms in a BAM file + GTF file?
rnaseq
scRNA-seq
single-cell
genomics
ngs
updated 17 months ago by
GenoMax
145k • written 17 months ago by
O.rka
▴ 740
0
votes
0
replies
394
views
Why did I get more unique genes than unique transcripts w/ STAR -> featureCounts?
rnaseq
genomics
star
fastq
alignment
17 months ago by
O.rka
▴ 740
0
votes
1
reply
1.4k
views
Comment:
Comment: How do you download from CyVerse using FTP or wget?
17 months ago by
O.rka
▴ 740
0
votes
2
replies
1.4k
views
Comment:
Comment: How do you download from CyVerse using FTP or wget?
17 months ago by
O.rka
▴ 740
8
votes
6
replies
1.4k
views
How do you download from CyVerse using FTP or wget?
cyverse
updated 17 months ago by
Ram
44k • written 17 months ago by
O.rka
▴ 740
410 results • Page
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