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470
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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
2.1 years ago by O.rka ▴ 720
0
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3
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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
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1
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469
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How does BUSCO convert MetaEuk identifiers?
calls metagenomics gene eukaryotic metatranscriptomics binning
2.2 years ago by O.rka ▴ 720
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0
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469
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Answer: Answer: How does BUSCO convert MetaEuk identifiers?
2.2 years ago by O.rka ▴ 720
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0
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5.5k
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Comment: Comment: Create smaller bam file based on the list of sequences
2.2 years ago by O.rka ▴ 720
0
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0
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392
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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
2.2 years ago by O.rka ▴ 720
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0
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7.2k
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Comment: Comment: Conversion from tdf to bed format
2.2 years ago by O.rka ▴ 720
0
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0
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488
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Comment: Comment: Can I download a partial database or delete subdirectories from an existing BUSC
2.2 years ago by O.rka ▴ 720
0
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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
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1
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488
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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
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3
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918
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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
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0
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918
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Comment: Comment: How to go from GenBank assembly identifier to taxonomic name? (Python or CLI)
2.2 years ago by O.rka ▴ 720
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0
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1.2k
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Comment: Comment: Extract the longest isoform from transcripts.fasta (rnaSPAdes output)
2.2 years ago by O.rka ▴ 720
3
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1
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1.2k
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Answer: Answer: Extract the longest isoform from transcripts.fasta (rnaSPAdes output)
2.2 years ago by O.rka ▴ 720
0
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1
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1.1k
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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
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0
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331
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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
0
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0
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1.2k
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Comment: Comment: Is there a tool that will tell me how "complex" (e.g., number of unique k-mers)
2.2 years ago by O.rka ▴ 720
0
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1
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1.2k
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Comment: Comment: Is there a tool that will tell me how "complex" (e.g., number of unique k-mers)
2.2 years ago by O.rka ▴ 720
3
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5
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3.0k
views
Where can I download ALL pfam flat-file annotations?
pfam annotations domain flat-files
updated 2.2 years ago by • 0 • written 5.5 years ago by ▴ 720
2
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6
replies
1.2k
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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
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3
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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
0
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0
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1.0k
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Comment: Comment: Where can I find an annotation table for human gencode ensemble gene ids to gene
2.3 years ago by O.rka ▴ 720
3
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4
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1.1k
views
What are some good uses of [sorted].bam files after RNA-seq?
genomics rnaseq fastq
updated 2.3 years ago by 43k • written 2.3 years ago by ▴ 720
0
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1
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9.0k
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Comment: Comment: featureCounts isoform vs gene summarization
2.3 years ago by O.rka ▴ 720
0
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0
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392
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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
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0
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436
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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
0
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1
reply
1.1k
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Comment: Comment: Any alternatives to BBMap's clumpify.sh program to optimize gzip compression?
2.3 years ago by O.rka ▴ 720
0
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1
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1.1k
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Comment: Comment: Any alternatives to BBMap's clumpify.sh program to optimize gzip compression?
2.3 years ago by O.rka ▴ 720
1
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6
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1.1k
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Any alternatives to BBMap's clumpify.sh program to optimize gzip compression?
fastq genomics rnaseq
updated 2.3 years ago by 142k • written 2.3 years ago by ▴ 720
1
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1
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1.2k
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Comment: Comment: How to get consensus annotations for a de novo orthogroup/ortholog analysis?
2.4 years ago by O.rka ▴ 720
1
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1
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1.2k
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Comment: Comment: How to get consensus annotations for a de novo orthogroup/ortholog analysis?
2.4 years ago by O.rka ▴ 720
3
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5
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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
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0
replies
697
views
Comment: Comment: How can I test whether a treatment truncates transcript length using transcripto
2.4 years ago by O.rka ▴ 720
0
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2
replies
697
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How can I test whether a treatment truncates transcript length using transcriptomics?
genomics transcriptomics statistics
2.4 years ago by O.rka ▴ 720
0
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0
replies
1.1k
views
Comment: Comment: How to download BBTools sketch databases using fetchRefSeq?
2.6 years ago by O.rka ▴ 720
0
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0
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459
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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
2.6 years ago by O.rka ▴ 720
0
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1
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1.1k
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Comment: Comment: How to download BBTools sketch databases using fetchRefSeq?
2.6 years ago by O.rka ▴ 720
0
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4
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1.1k
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How to download BBTools sketch databases using fetchRefSeq?
metagenomics bbmap sketch bbtools
2.6 years ago by O.rka ▴ 720
0
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1
reply
14k
views
Comment: Comment: BBSketch - A Tool for Rapid Sequence Comparison
2.6 years ago by O.rka ▴ 720
1
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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
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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
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4
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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
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0
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1.2k
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Answer: Answer: How to adapt a for loop of `muscle` alignments using GNU Parallel?
2.6 years ago by O.rka ▴ 720
0
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0
replies
1.9k
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Comment: Comment: Recommended approach for building phylogenetic tree from de novo metagenomes
2.6 years ago by O.rka ▴ 720
0
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0
replies
17k
views
Comment: Comment: How To Add Specific Word To Fasta Header
2.6 years ago by O.rka ▴ 720
1
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4
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1.9k
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Recommended approach for building phylogenetic tree from de novo metagenomes
phylogenetic tree Metagenomics
2.6 years ago by O.rka ▴ 720
0
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0
replies
1.9k
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Comment: Comment: Recommended approach for building phylogenetic tree from de novo metagenomes
2.6 years ago by O.rka ▴ 720
4
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2
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1.9k
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What is the recommended way to subsample Oxford Nanopore (ONT) fastq reads with matching fast5?
sequencing
2.7 years ago by O.rka ▴ 720
2
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0
replies
1.9k
views
Answer: Answer: What is the recommended way to subsample Oxford Nanopore (ONT) fastq reads with
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 ▴ 540 • written 2.8 years ago by ▴ 720
409 results • Page 3 of 9
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