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3
votes
2
replies
999
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
663
views
What are the suggested parameters for running IQ-TREE on a protein alignment for phylogeny?
protein metagenomics phylogeny iqtree
updated 2.1 years ago by ★ 27k • written 2.1 years ago by ▴ 720
0
votes
0
replies
473
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
2.2 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 6.4k • written 2.2 years ago by ▴ 720
1
vote
1
reply
472
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
397
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
392
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
493
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
929
views
How to go from GenBank assembly identifier to taxonomic name? (Python or CLI)
taxonomy metagenomics database genbank
updated 2.2 years ago by 100k • written 2.2 years ago by ▴ 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 142k • written 2.2 years ago by ▴ 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
3.1k
views
Where can I download ALL pfam flat-file annotations?
pfam annotations domain flat-files
updated 2.3 years ago by • 0 • written 5.5 years ago by ▴ 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
2.3 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 2.4 years ago by 44k • written 2.4 years ago by ▴ 720
0
votes
0
replies
397
views
How do you use ERCC spike-ins for ALR Transformation of RNA-seq data?
fastq genomics rnaseq
2.4 years ago by O.rka ▴ 720
0
votes
0
replies
441
views
How to find "consensus classification" for a cluster of highly similar metagenome assembled genomes [MAG]?
metatranscriptomics classification binning metagenomics
2.4 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 142k • written 2.4 years ago by ▴ 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 ★ 2.5k • written 2.4 years ago by ▴ 720
0
votes
2
replies
701
views
How can I test whether a treatment truncates transcript length using transcriptomics?
genomics transcriptomics statistics
2.5 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
1.2k
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 ★ 27k • written 2.6 years ago by ▴ 720
0
votes
0
replies
479
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
978
views
How does MetaProdigal handle metagenomics where different genetic codes are used?
metagenomics metatranscriptomics binning
updated 2.7 years ago by ▴ 540 • written 2.8 years ago by ▴ 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 2.8 years ago by ▴ 710 • written 7.8 years ago by ▴ 720
2
votes
3
replies
2.2k
views
How to compute module completion ratio of KEGG modules from KO identifiers? (command line)
database
updated 2.8 years ago by ▴ 540 • written 4.1 years ago by ▴ 720
0
votes
3
replies
905
views
What is the best way to get all bacteria proteins from nr?
protists database nr
updated 2.8 years ago by 142k • written 2.8 years ago by ▴ 720
2
votes
2
replies
1.5k
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
523
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 ▴ 590 • written 2.8 years ago by ▴ 720
3
votes
3
replies
1.4k
views
How do you split metagenomic bins/MAGs into eukaryotic and prokaryotic?
protist metagenomics prokaryotic eukaryotic gtdbtk
updated 2.8 years ago by ★ 27k • written 2.8 years ago by ▴ 720
3
votes
1
reply
967
views
Clarification on KEGG orthologs, why don't all have KEGG modules?
ortholog database kegg
updated 2.9 years ago by 3.6k • written 2.9 years ago by ▴ 720
1
vote
4
replies
721
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
634
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
514
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
1.5k
views
How to structure my edgeR model to incorporate a temporal variable and 2 categorical variables?
edgeR differential-gene-expression glm r
3.1 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 88k • written 3.1 years ago by ▴ 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 • 0 • written 4.3 years ago by ▴ 720
0
votes
0
replies
582
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
993
views
How to create a dummy GFF file from fasta?
fasta coverage bed gff
3.2 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 ▴ 310 • written 3.2 years ago by ▴ 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 ★ 27k • written 3.2 years ago by ▴ 720
0
votes
0
replies
497
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 ▴ 270 • written 3.2 years ago by ▴ 720
0
votes
0
replies
644
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 44k • written 3.2 years ago by ▴ 720
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