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Showing :
questions
3
votes
2
replies
989
views
How can I get a taxid from an assembly id (e.g., GCA_003223415.1 -> 2026742)
metagenomics
accession
ncbi
taxonomy
database
2.0 years ago by
O.rka
▴ 720
3
votes
1
reply
654
views
What are the suggested parameters for running IQ-TREE on a protein alignment for phylogeny?
protein
metagenomics
phylogeny
iqtree
updated 2.0 years ago by
Mensur Dlakic
★ 27k • written 2.0 years ago by
O.rka
▴ 720
0
votes
0
replies
471
views
Does anyone know how to filter by strategy on NCBI's search in BioProject/SRA? (e.g., no amplicons)
search
metagenomics
sra
ncbi
meta
2.1 years ago by
O.rka
▴ 720
0
votes
3
replies
1.5k
views
How to check Fasta file ASCII characters and fix encoding errors?
genomics
fasta
fastq
updated 2.2 years ago by
colindaven
6.4k • written 2.2 years ago by
O.rka
▴ 720
1
vote
1
reply
470
views
How does BUSCO convert MetaEuk identifiers?
calls
metagenomics
gene
eukaryotic
metatranscriptomics
binning
2.2 years ago by
O.rka
▴ 720
0
votes
0
replies
392
views
Does anyone know how to get the headers for a bam.tdf file converted to a bedgraph file?
bedgraph
tdf
bam
igv
2.2 years ago by
O.rka
▴ 720
0
votes
0
replies
387
views
Does anyone know how to run EUKulele with an existing database?
eukaryotic
metagenomics
database
annotation
2.2 years ago by
O.rka
▴ 720
0
votes
1
reply
489
views
Can I download a partial database or delete subdirectories from an existing BUSCO v5 database?
metagenomics
metatranscriptomics
annotation
2.2 years ago by
O.rka
▴ 720
6
votes
3
replies
921
views
How to go from GenBank assembly identifier to taxonomic name? (Python or CLI)
taxonomy
metagenomics
database
genbank
updated 2.2 years ago by
Istvan Albert
100k • written 2.2 years ago by
O.rka
▴ 720
0
votes
1
reply
1.1k
views
Where can I find prebuilt diamond databases that also contain taxonomy information?
taxonomy
database
diamond
alignment
protein
updated 2.2 years ago by
GenoMax
142k • written 2.2 years ago by
O.rka
▴ 720
0
votes
0
replies
331
views
Is there a similar option to Diamond's --max-target-seqs in MMSeqs2?
metagenomics
diamond
blastp
alignment
mmseqs2
2.2 years ago by
O.rka
▴ 720
3
votes
5
replies
3.0k
views
Where can I download ALL pfam flat-file annotations?
pfam
annotations
domain
flat-files
updated 2.3 years ago by
mwylerCH
• 0 • written 5.5 years ago by
O.rka
▴ 720
2
votes
6
replies
1.2k
views
Is there a tool that will tell me how "complex" (e.g., number of unique k-mers) are in a fastq file?
genomics
rnaseq
fastq
2.2 years ago by
O.rka
▴ 720
2
votes
3
replies
1.0k
views
Where can I find an annotation table for human gencode ensemble gene ids to gene name/description?
fastq
annotation
genomics
rnaseq
2.3 years ago by
O.rka
▴ 720
3
votes
4
replies
1.1k
views
What are some good uses of [sorted].bam files after RNA-seq?
genomics
rnaseq
fastq
updated 2.3 years ago by
Ram
43k • written 2.3 years ago by
O.rka
▴ 720
0
votes
0
replies
393
views
How do you use ERCC spike-ins for ALR Transformation of RNA-seq data?
fastq
genomics
rnaseq
2.3 years ago by
O.rka
▴ 720
0
votes
0
replies
436
views
How to find "consensus classification" for a cluster of highly similar metagenome assembled genomes [MAG]?
metatranscriptomics
classification
binning
metagenomics
2.3 years ago by
O.rka
▴ 720
1
vote
6
replies
1.1k
views
Any alternatives to BBMap's clumpify.sh program to optimize gzip compression?
fastq
genomics
rnaseq
updated 2.4 years ago by
GenoMax
142k • written 2.4 years ago by
O.rka
▴ 720
3
votes
5
replies
1.2k
views
How to get consensus annotations for a de novo orthogroup/ortholog analysis?
metatranscriptomics
metagenomics
transcriptomics
updated 2.4 years ago by
Dunois
★ 2.5k • written 2.4 years ago by
O.rka
▴ 720
0
votes
2
replies
697
views
How can I test whether a treatment truncates transcript length using transcriptomics?
genomics
transcriptomics
statistics
2.4 years ago by
O.rka
▴ 720
0
votes
0
replies
459
views
Are there any studies that have computed the distribution on number of samples vs. number of features in Omics datasets?
metatranscriptomics
metagenomics
statistics
genomics
2.6 years ago by
O.rka
▴ 720
0
votes
4
replies
1.1k
views
How to download BBTools sketch databases using fetchRefSeq?
metagenomics
bbmap
sketch
bbtools
2.6 years ago by
O.rka
▴ 720
1
vote
1
reply
2.2k
views
How to merge HMM files for HMMSearch?
alignment
hmm
protein
annotation
updated 2.6 years ago by
Mensur Dlakic
★ 27k • written 2.6 years ago by
O.rka
▴ 720
0
votes
0
replies
478
views
Any ORF callers that have an option to choose first N ORFs?
metagenomics
genomics
metatranscriptomics
2.6 years ago by
O.rka
▴ 720
1
vote
4
replies
1.2k
views
How to adapt a for loop of `muscle` alignments using GNU Parallel?
alignment
bash
parallel
2.6 years ago by
O.rka
▴ 720
1
vote
4
replies
1.9k
views
Recommended approach for building phylogenetic tree from de novo metagenomes
phylogenetic
tree
Metagenomics
2.6 years ago by
O.rka
▴ 720
4
votes
2
replies
1.9k
views
What is the recommended way to subsample Oxford Nanopore (ONT) fastq reads with matching fast5?
sequencing
2.7 years ago by
O.rka
▴ 720
0
votes
1
reply
972
views
How does MetaProdigal handle metagenomics where different genetic codes are used?
metagenomics
metatranscriptomics
binning
updated 2.7 years ago by
Tom
▴ 540 • written 2.8 years ago by
O.rka
▴ 720
1
vote
2
replies
2.4k
views
Where to download a table of operons with genes for E. coli?
operon
genes
e coli
transcription
units
updated 2.7 years ago by
rioualen
▴ 710 • written 7.8 years ago by
O.rka
▴ 720
2
votes
3
replies
2.2k
views
How to compute module completion ratio of KEGG modules from KO identifiers? (command line)
database
updated 2.7 years ago by
Tom
▴ 540 • written 4.1 years ago by
O.rka
▴ 720
0
votes
3
replies
897
views
What is the best way to get all bacteria proteins from nr?
protists
database
nr
updated 2.8 years ago by
GenoMax
142k • written 2.8 years ago by
O.rka
▴ 720
2
votes
2
replies
1.4k
views
Would you use HMMSCAN or HMMSEARCH when the query is much larger than the database?
nr
hmmsearch
hmmer
hmm
hmmscan
2.8 years ago by
O.rka
▴ 720
0
votes
0
replies
521
views
Does anyone have any experience in hacking MaxBin2 to handle custom marker sets?
metagenomics
maxbin2
binning
2.8 years ago by
O.rka
▴ 720
1
vote
6
replies
1.2k
views
How to group transcripts by "gene" from different transcript assemblies?
assembly
trinity
rnaspades
transcript
updated 2.8 years ago by
ponganta
▴ 590 • written 2.8 years ago by
O.rka
▴ 720
3
votes
3
replies
1.3k
views
How do you split metagenomic bins/MAGs into eukaryotic and prokaryotic?
protist
metagenomics
prokaryotic
eukaryotic
gtdbtk
updated 2.8 years ago by
Mensur Dlakic
★ 27k • written 2.8 years ago by
O.rka
▴ 720
3
votes
1
reply
963
views
Clarification on KEGG orthologs, why don't all have KEGG modules?
ortholog
database
kegg
updated 2.9 years ago by
andres.firrincieli
3.6k • written 2.9 years ago by
O.rka
▴ 720
1
vote
4
replies
717
views
What is the best short reader to very large reference fasta?
mapping
alignment
fastq
bowtie2
bwa
read
2.9 years ago by
O.rka
▴ 720
1
vote
0
replies
628
views
Discussion on binning multiple metagenomes at the same time?
binning
metagenomics
mags
3.0 years ago by
O.rka
▴ 720
0
votes
0
replies
511
views
How to use transcript coverage for ORF calls on contig?
gene-calling
virus
metatranscriptomics
metagenomics
3.0 years ago by
O.rka
▴ 720
1
vote
4
replies
2.2k
views
How to calculate differential methylation from nanopore reads?
sequencing
methylation
3.0 years ago by
O.rka
▴ 720
5
votes
6
replies
1.4k
views
How to structure my edgeR model to incorporate a temporal variable and 2 categorical variables?
edgeR
differential-gene-expression
glm
r
3.0 years ago by
O.rka
▴ 720
1
vote
2
replies
1.5k
views
Understanding why `Design matrix not of full rank. The following coefficients not estimable` during GLM
edgeR
design-matrix
differential
glm
offtopic
updated 3.1 years ago by
Kevin Blighe
88k • written 3.1 years ago by
O.rka
▴ 720
5
votes
4
replies
11k
views
Why is `send` lower than `sstart` from blast format 6 output?
blast
genomics
updated 3.1 years ago by
David
• 0 • written 4.3 years ago by
O.rka
▴ 720
0
votes
0
replies
580
views
How to calculate differential coverage between two groups?
differential
bed
bam
rnaseq
coverage
3.1 years ago by
O.rka
▴ 720
0
votes
1
reply
985
views
How to create a dummy GFF file from fasta?
fasta
coverage
bed
gff
3.1 years ago by
O.rka
▴ 720
0
votes
1
reply
1.0k
views
What does the -0 flag of samtools fastq mean?
samtools
updated 3.2 years ago by
aw7
▴ 300 • written 3.2 years ago by
O.rka
▴ 720
0
votes
2
replies
1.5k
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
kegg
database
metagenomics
module
updated 3.2 years ago by
Mensur Dlakic
★ 27k • written 3.2 years ago by
O.rka
▴ 720
0
votes
0
replies
496
views
What do the + and - mean in KEGG Ortholog combinations under a particular Module?
kegg
database
module
ortholog
identifiers
3.2 years ago by
O.rka
▴ 720
4
votes
3
replies
2.0k
views
How to get a mapping between KEGG module and KEGG orthologs?
KEGG
Annotation
Ortholog
Module
updated 3.2 years ago by
Elucidata
▴ 270 • written 3.2 years ago by
O.rka
▴ 720
0
votes
0
replies
642
views
Should "dispersion" in edgeR be calculated for entire dataset or just conditions being analyzed?
differential-gene-expression
edgeR
RNA-Seq
updated 3 months ago by
Ram
43k • written 3.2 years ago by
O.rka
▴ 720
193 results • Page
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