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questions
0
votes
0
replies
142
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
5 days ago by
O.rka
▴ 710
1
vote
3
replies
398
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 7 days ago by
Mensur Dlakic
★ 27k • written 9 days ago by
O.rka
▴ 710
0
votes
2
replies
335
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
22 days ago by
O.rka
▴ 710
0
votes
2
replies
344
views
Why are gene models from JGI non-sense when using AGAT to to extract proteins?
translation
models
gif
gene
cgi
4 weeks ago by
O.rka
▴ 710
1
vote
1
reply
508
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 10 weeks ago by
akshay
▴ 10 • written 5 months ago by
O.rka
▴ 710
0
votes
1
reply
574
views
How can I calculate the percent of bases covered in the query assembly relative to the reference assembly?
samtools
updated 3 months ago by
dthorbur
★ 1.9k • written 3 months ago by
O.rka
▴ 710
1
vote
2
replies
665
views
How to use Nextflow to call scripts from different environments?
anaconda
conda
nextflow
4 months ago by
O.rka
▴ 710
2
votes
1
reply
476
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam
sam
reads
fastq
updated 5 months ago by
rpolicastro
13k • written 5 months ago by
O.rka
▴ 710
2
votes
3
replies
719
views
How to check if my sequence is DNA or Protein in BioPython?
genomics
biopython
fasta
updated 5 months ago by
Joe
21k • written 5 months ago by
O.rka
▴ 710
1
vote
1
reply
616
views
How to download taxonomy/lineage/taxonid information for JGI genome organism codes? (e.g., MycoCosm and PhycoCosm)
jgi
genomics
phycocosm
mycocosm
taxonomy
6 months ago by
O.rka
▴ 710
0
votes
2
replies
559
views
Why are some HUMAnN features in [name]_pathabundance.tsv missing taxonomy?
metagenomics
metabolism
humann
biobakery
metatranscriptomics
6 months ago by
O.rka
▴ 710
0
votes
1
reply
462
views
How to download genomes and proteins from JGI in bulk via the command line?
jgi
cli
updated 7 months ago by
Ram
43k • written 7 months ago by
O.rka
▴ 710
1
vote
3
replies
681
views
How to convert between UniRef50 to EC/enzyme number?
Uniref
conversion
uniprot
enzyme
updated 7 months ago by
Elisabeth Gasteiger
★ 2.4k • written 7 months ago by
O.rka
▴ 710
0
votes
2
replies
690
views
How to run TRUST4 for BCR/TCR detection using 10X data?
immunology
trust4
illumina
10x
7 months ago by
O.rka
▴ 710
7
votes
9
replies
1.9k
views
6 follow
How can I transfer gene models to a new assembly?
gene
Assembly
updated 8 months ago by
Philipp Bayer
8.4k • written 4.1 years ago by
O.rka
▴ 710
3
votes
3
replies
805
views
When counting ASVs in DADA2, does a hit/count only occur at 100% alignment percent identity?
metagenomics
qiime2
amplicon
16s
dada2
updated 8 months ago by
andres.firrincieli
3.6k • written 8 months ago by
O.rka
▴ 710
0
votes
0
replies
353
views
What criteria are used to determine significant HMMER hits?
kegg
protein
kofamscan
annotation
metagenomics
9 months ago by
O.rka
▴ 710
0
votes
1
reply
605
views
Using tRNAscan-SE for mitochondria tRNA from microeukaryotes like protists and yeast?
trnascan
yeasts
eukaryotes
protists
trna
updated 10 months ago by
shelkmike
★ 1.2k • written 10 months ago by
O.rka
▴ 710
3
votes
2
replies
2.1k
views
Help speeding up HMMER's HMMSearch algorithm for large fasta file with GNU Parallel
protein
parallel
hmmer
hmm
bash
updated 10 months ago by
lieven.sterck
15k • written 2.7 years ago by
O.rka
▴ 710
0
votes
7
replies
1.7k
views
How can I speed up wget from UniProt for UniRef90/50 fasta?
wget
download
uniprot
uniref
updated 11 months ago by
Mensur Dlakic
★ 27k • written 11 months ago by
O.rka
▴ 710
4
votes
6
replies
1.2k
views
Should you specify "-p" for paired end reads using featureCounts?
fastq
rnaseq
genomics
12 months ago by
O.rka
▴ 710
0
votes
0
replies
291
views
How can I get taxa relative abundances from HUMAnN?
metagenomics
humann
biobakery
metatranscriptomics
13 months ago by
O.rka
▴ 710
5
votes
9
replies
2.1k
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 9 months ago by
GenoMax
142k • written 13 months ago by
O.rka
▴ 710
0
votes
5
replies
903
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 13 months ago by
GenoMax
142k • written 13 months ago by
O.rka
▴ 710
0
votes
0
replies
352
views
Why did I get more unique genes than unique transcripts w/ STAR -> featureCounts?
rnaseq
genomics
star
fastq
alignment
13 months ago by
O.rka
▴ 710
8
votes
6
replies
1.2k
views
How do you download from CyVerse using FTP or wget?
cyverse
updated 13 months ago by
Ram
43k • written 13 months ago by
O.rka
▴ 710
3
votes
3
replies
2.2k
views
How to fix "Please indicate the file directory in 'setting' file?" for MaxBin2?
maxbin2
binning
metagenomics
updated 12 months ago by
Ram
43k • written 2.9 years ago by
O.rka
▴ 710
1
vote
4
replies
2.0k
views
How could I "recreate" UniRef50/UniRef90 with MMSEQS2?
clustering
proteins
annotation
mmseqs2
updated 9 months ago by
Zachary
• 0 • written 14 months ago by
O.rka
▴ 710
1
vote
2
replies
1.9k
views
Are there any tools that can create a very basic GTF file from contig sequences (no annotations really needed) ?
Assembly
mapping
14 months ago by
O.rka
▴ 710
0
votes
0
replies
373
views
What's the state-of-the-art for gene calling in eukaryotic transcriptomics?
modeling
eukaryotic
transcriptomics
call
gene
15 months ago by
O.rka
▴ 710
3
votes
5
replies
1.1k
views
How can I run multiple sequence alignment for a large number of proteins (~10k)
muscle
msa
protein
multiple
alignment
sequence
updated 15 months ago by
Mensur Dlakic
★ 27k • written 16 months ago by
O.rka
▴ 710
1
vote
2
replies
642
views
What's best practice when determining a degenerate base when creating a primer?
primer-design
alignment
genomics
16 months ago by
O.rka
▴ 710
1
vote
6
replies
1.4k
views
Any command line tools that can design primers from a multiple sequence alignment?
primer-design
genomics
cli
16 months ago by
O.rka
▴ 710
9
votes
6
replies
1.5k
views
What in silico PCR commandline tool do you use that can handle IUPAC characters?
pcr
amplicon
primer
updated 4 weeks ago by
Ram
43k • written 16 months ago by
O.rka
▴ 710
3
votes
3
replies
776
views
How to find full length ribosomal sequences for fungi?
ncbi
ribosomal
fungi
nt
16 months ago by
O.rka
▴ 710
0
votes
0
replies
323
views
How to estimate the memory requirements for Diamond given the database and query protein sizes?
alignment
diamond
memory
requirements
16 months ago by
O.rka
▴ 710
0
votes
4
replies
685
views
How to "enrich" a large set of proteins (>11M) for protein hits in UniRef90?
uniref
proteins
alignment
16 months ago by
O.rka
▴ 710
3
votes
4
replies
1.3k
views
How to extract unmapped reads if you have paired end reads (fastq) and mapped BAM file?
fastq
bam
sam
reads
18 months ago by
O.rka
▴ 710
2
votes
2
replies
868
views
What's the benefit of using the `no_alt_analysis_set` Bowtie2 index over the primary assembly?
human
rnaseq
mapping
metagenomics
updated 18 months ago by
ATpoint
82k • written 18 months ago by
O.rka
▴ 710
0
votes
1
reply
678
views
Is there a tool that quantifies “spatial coverage”, that is what percentage of a reference assembly has a read mapped to it?
coverage
genomics
mapping
assembly
updated 20 months ago by
GenoMax
142k • written 20 months ago by
O.rka
▴ 710
0
votes
2
replies
550
views
How to calculate position-specific fastq stats?
rnaseq
fastq
metagenomics
genomics
21 months ago by
O.rka
▴ 710
0
votes
3
replies
1.6k
views
Are there any tools that automatically detect where to truncate forward and reverse reads for 16S (DADA2)?
16s
dada2
illumina
metagenomics
qiime2
21 months ago by
O.rka
▴ 710
1
vote
3
replies
1.2k
views
Is it required for all sequences to be same length when clustering OTUs in metagenomics (ONT Nanopore)
otu
metagenomics
clustering
nanopore
updated 21 months ago by
antonioggsousa
3.2k • written 21 months ago by
O.rka
▴ 710
0
votes
2
replies
629
views
What percent identity is recommended for detecting protein homology within a species?
alignment
genomics
proteomics
21 months ago by
O.rka
▴ 710
1
vote
6
replies
1.6k
views
Is there a tool that calculates genome coverage? (e.g., 1X, 10X, 100X)
ncbi
metagenomics
submission
22 months ago by
O.rka
▴ 710
0
votes
1
reply
477
views
Software to produce position-specific conservation of multiple sequence alignment results?
transcriptomics
genomics
alignment
proteomics
updated 22 months ago by
Mensur Dlakic
★ 27k • written 22 months ago by
O.rka
▴ 710
0
votes
1
reply
1.0k
views
How to count the number of multimapped reads from a bam file?
rnaseq
mapping
bowtie2
featurecounts
updated 22 months ago by
Shred
★ 1.4k • written 22 months ago by
O.rka
▴ 710
1
vote
1
reply
928
views
Advice on mapping reads to polyploid de-novo assembly
assembly
RNA-Seq
updated 23 months ago by
colindaven
6.4k • written 4.3 years ago by
O.rka
▴ 710
0
votes
1
reply
579
views
How do you predict regions on a protein that are exposed on the cell surface?
protein
antibody
hmm
domain
updated 23 months ago by
Mensur Dlakic
★ 27k • written 23 months ago by
O.rka
▴ 710
3
votes
2
replies
967
views
How can I get a taxid from an assembly id (e.g., GCA_003223415.1 -> 2026742)
metagenomics
accession
ncbi
taxonomy
database
24 months ago by
O.rka
▴ 710
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