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4.8k
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Comment: Comment: What are the recommended methods for merging de-novo assemblies?
2.6 years ago by O.rka ▴ 740
0
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0
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538
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Does anyone know how to filter by strategy on NCBI's search in BioProject/SRA? (e.g., no amplicons)
search metagenomics sra ncbi meta
2.7 years ago by O.rka ▴ 740
0
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3
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1.8k
views
How to check Fasta file ASCII characters and fix encoding errors?
genomics fasta fastq
updated 2.7 years ago by 7.0k • written 2.7 years ago by ▴ 740
1
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1
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567
views
How does BUSCO convert MetaEuk identifiers?
calls metagenomics gene eukaryotic metatranscriptomics binning
2.7 years ago by O.rka ▴ 740
1
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0
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567
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Answer: Answer: How does BUSCO convert MetaEuk identifiers?
2.7 years ago by O.rka ▴ 740
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0
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6.1k
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Comment: Comment: Create smaller bam file based on the list of sequences
2.7 years ago by O.rka ▴ 740
0
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0
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482
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Does anyone know how to get the headers for a bam.tdf file converted to a bedgraph file?
bedgraph tdf bam igv
2.8 years ago by O.rka ▴ 740
0
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0
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7.6k
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Comment: Comment: Conversion from tdf to bed format
2.8 years ago by O.rka ▴ 740
0
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0
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578
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Comment: Comment: Can I download a partial database or delete subdirectories from an existing BUSC
2.8 years ago by O.rka ▴ 740
0
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0
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489
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Does anyone know how to run EUKulele with an existing database?
eukaryotic metagenomics database annotation
2.8 years ago by O.rka ▴ 740
0
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1
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578
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Can I download a partial database or delete subdirectories from an existing BUSCO v5 database?
metagenomics metatranscriptomics annotation
2.8 years ago by O.rka ▴ 740
6
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3
replies
1.1k
views
How to go from GenBank assembly identifier to taxonomic name? (Python or CLI)
taxonomy metagenomics database genbank
updated 2.8 years ago by 102k • written 2.8 years ago by ▴ 740
0
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0
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1.1k
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Comment: Comment: How to go from GenBank assembly identifier to taxonomic name? (Python or CLI)
2.8 years ago by O.rka ▴ 740
0
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0
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1.4k
views
Comment: Comment: Extract the longest isoform from transcripts.fasta (rnaSPAdes output)
2.8 years ago by O.rka ▴ 740
3
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1
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1.4k
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Answer: Answer: Extract the longest isoform from transcripts.fasta (rnaSPAdes output)
2.8 years ago by O.rka ▴ 740
0
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1
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1.2k
views
Where can I find prebuilt diamond databases that also contain taxonomy information?
taxonomy database diamond alignment protein
updated 2.8 years ago by 148k • written 2.8 years ago by ▴ 740
0
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0
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415
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Is there a similar option to Diamond's --max-target-seqs in MMSeqs2?
metagenomics diamond blastp alignment mmseqs2
2.8 years ago by O.rka ▴ 740
0
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0
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1.3k
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Comment: Comment: Is there a tool that will tell me how "complex" (e.g., number of unique k-mers)
2.8 years ago by O.rka ▴ 740
0
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1
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1.3k
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Comment: Comment: Is there a tool that will tell me how "complex" (e.g., number of unique k-mers)
2.8 years ago by O.rka ▴ 740
3
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5
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3.3k
views
Where can I download ALL pfam flat-file annotations?
pfam annotations domain flat-files
updated 2.8 years ago by • 0 • written 6.1 years ago by ▴ 740
2
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6
replies
1.3k
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
2.8 years ago by O.rka ▴ 740
2
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3
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1.2k
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Where can I find an annotation table for human gencode ensemble gene ids to gene name/description?
fastq annotation genomics rnaseq
2.9 years ago by O.rka ▴ 740
0
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0
replies
1.2k
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Comment: Comment: Where can I find an annotation table for human gencode ensemble gene ids to gene
2.9 years ago by O.rka ▴ 740
3
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4
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1.3k
views
What are some good uses of [sorted].bam files after RNA-seq?
genomics rnaseq fastq
updated 2.9 years ago by 44k • written 2.9 years ago by ▴ 740
0
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1
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9.5k
views
Comment: Comment: featureCounts isoform vs gene summarization
2.9 years ago by O.rka ▴ 740
0
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0
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461
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How do you use ERCC spike-ins for ALR Transformation of RNA-seq data?
fastq genomics rnaseq
2.9 years ago by O.rka ▴ 740
0
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0
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521
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How to find "consensus classification" for a cluster of highly similar metagenome assembled genomes [MAG]?
metatranscriptomics classification binning metagenomics
2.9 years ago by O.rka ▴ 740
0
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1
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1.3k
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Comment: Comment: Any alternatives to BBMap's clumpify.sh program to optimize gzip compression?
2.9 years ago by O.rka ▴ 740
0
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1
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1.3k
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Comment: Comment: Any alternatives to BBMap's clumpify.sh program to optimize gzip compression?
2.9 years ago by O.rka ▴ 740
1
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6
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1.3k
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Any alternatives to BBMap's clumpify.sh program to optimize gzip compression?
fastq genomics rnaseq
updated 2.9 years ago by 148k • written 2.9 years ago by ▴ 740
1
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1
reply
1.4k
views
Comment: Comment: How to get consensus annotations for a de novo orthogroup/ortholog analysis?
3.0 years ago by O.rka ▴ 740
1
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1
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1.4k
views
Comment: Comment: How to get consensus annotations for a de novo orthogroup/ortholog analysis?
3.0 years ago by O.rka ▴ 740
3
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5
replies
1.4k
views
How to get consensus annotations for a de novo orthogroup/ortholog analysis?
metatranscriptomics metagenomics transcriptomics
updated 3.0 years ago by ★ 2.8k • written 3.0 years ago by ▴ 740
0
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0
replies
779
views
Comment: Comment: How can I test whether a treatment truncates transcript length using transcripto
3.0 years ago by O.rka ▴ 740
0
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2
replies
779
views
How can I test whether a treatment truncates transcript length using transcriptomics?
genomics transcriptomics statistics
3.0 years ago by O.rka ▴ 740
0
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0
replies
1.3k
views
Comment: Comment: How to download BBTools sketch databases using fetchRefSeq?
3.1 years ago by O.rka ▴ 740
0
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0
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515
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Are there any studies that have computed the distribution on number of samples vs. number of features in Omics datasets?
metatranscriptomics metagenomics statistics genomics
3.1 years ago by O.rka ▴ 740
0
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1
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1.3k
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Comment: Comment: How to download BBTools sketch databases using fetchRefSeq?
3.1 years ago by O.rka ▴ 740
0
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4
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1.3k
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How to download BBTools sketch databases using fetchRefSeq?
metagenomics bbmap sketch bbtools
3.1 years ago by O.rka ▴ 740
0
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1
reply
15k
views
Comment: Comment: BBSketch - A Tool for Rapid Sequence Comparison
3.2 years ago by O.rka ▴ 740
1
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1
reply
2.5k
views
How to merge HMM files for HMMSearch?
alignment hmm protein annotation
updated 3.2 years ago by ★ 28k • written 3.2 years ago by ▴ 740
0
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0
replies
542
views
Any ORF callers that have an option to choose first N ORFs?
metagenomics genomics metatranscriptomics
3.2 years ago by O.rka ▴ 740
1
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4
replies
1.4k
views
How to adapt a for loop of `muscle` alignments using GNU Parallel?
alignment bash parallel
3.2 years ago by O.rka ▴ 740
1
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0
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1.4k
views
Answer: Answer: How to adapt a for loop of `muscle` alignments using GNU Parallel?
3.2 years ago by O.rka ▴ 740
0
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0
replies
2.2k
views
Comment: Comment: Recommended approach for building phylogenetic tree from de novo metagenomes
3.2 years ago by O.rka ▴ 740
0
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0
replies
18k
views
Comment: Comment: How To Add Specific Word To Fasta Header
3.2 years ago by O.rka ▴ 740
1
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4
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2.2k
views
Recommended approach for building phylogenetic tree from de novo metagenomes
phylogenetic tree Metagenomics
3.2 years ago by O.rka ▴ 740
0
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0
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2.2k
views
Comment: Comment: Recommended approach for building phylogenetic tree from de novo metagenomes
3.2 years ago by O.rka ▴ 740
4
votes
2
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2.1k
views
What is the recommended way to subsample Oxford Nanopore (ONT) fastq reads with matching fast5?
sequencing
3.2 years ago by O.rka ▴ 740
2
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0
replies
2.1k
views
Answer: Answer: What is the recommended way to subsample Oxford Nanopore (ONT) fastq reads with
3.2 years ago by O.rka ▴ 740
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