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6.1k
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Comment: Comment: What are the recommended methods for merging de-novo assemblies?
3.4 years ago by O.rka ▴ 750
0
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0
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653
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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
3.5 years ago by O.rka ▴ 750
0
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3
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2.4k
views
How to check Fasta file ASCII characters and fix encoding errors?
genomics fasta fastq
updated 3.5 years ago by 7.9k • written 3.5 years ago by ▴ 750
1
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1
reply
746
views
How does BUSCO convert MetaEuk identifiers?
calls metagenomics gene eukaryotic metatranscriptomics binning
3.5 years ago by O.rka ▴ 750
1
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0
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746
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Answer: Answer: How does BUSCO convert MetaEuk identifiers?
3.5 years ago by O.rka ▴ 750
0
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0
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6.9k
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Comment: Comment: Create smaller bam file based on the list of sequences
3.5 years ago by O.rka ▴ 750
0
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0
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662
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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
3.5 years ago by O.rka ▴ 750
0
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0
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8.3k
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Comment: Comment: Conversion from tdf to bed format
3.5 years ago by O.rka ▴ 750
0
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0
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734
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Comment: Comment: Can I download a partial database or delete subdirectories from an existing BUSC
3.5 years ago by O.rka ▴ 750
0
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0
replies
623
views
Does anyone know how to run EUKulele with an existing database?
eukaryotic metagenomics database annotation
3.5 years ago by O.rka ▴ 750
0
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1
reply
734
views
Can I download a partial database or delete subdirectories from an existing BUSCO v5 database?
metagenomics metatranscriptomics annotation
3.5 years ago by O.rka ▴ 750
6
votes
3
replies
1.5k
views
How to go from GenBank assembly identifier to taxonomic name? (Python or CLI)
taxonomy metagenomics database genbank
updated 3.5 years ago by 103k • written 3.5 years ago by ▴ 750
0
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0
replies
1.5k
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Comment: Comment: How to go from GenBank assembly identifier to taxonomic name? (Python or CLI)
3.5 years ago by O.rka ▴ 750
0
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0
replies
1.9k
views
Comment: Comment: Extract the longest isoform from transcripts.fasta (rnaSPAdes output)
3.5 years ago by O.rka ▴ 750
3
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1
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1.9k
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Answer: Answer: Extract the longest isoform from transcripts.fasta (rnaSPAdes output)
3.5 years ago by O.rka ▴ 750
0
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1
reply
1.6k
views
Where can I find prebuilt diamond databases that also contain taxonomy information?
taxonomy database diamond alignment protein
updated 3.5 years ago by 153k • written 3.5 years ago by ▴ 750
0
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0
replies
596
views
Is there a similar option to Diamond's --max-target-seqs in MMSeqs2?
metagenomics diamond blastp alignment mmseqs2
3.5 years ago by O.rka ▴ 750
0
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0
replies
1.7k
views
Comment: Comment: Is there a tool that will tell me how "complex" (e.g., number of unique k-mers)
3.6 years ago by O.rka ▴ 750
0
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1
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1.7k
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Comment: Comment: Is there a tool that will tell me how "complex" (e.g., number of unique k-mers)
3.6 years ago by O.rka ▴ 750
3
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5
replies
3.8k
views
Where can I download ALL pfam flat-file annotations?
pfam annotations domain flat-files
updated 3.6 years ago by • 0 • written 6.8 years ago by ▴ 750
2
votes
6
replies
1.7k
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
3.6 years ago by O.rka ▴ 750
2
votes
3
replies
1.4k
views
Where can I find an annotation table for human gencode ensemble gene ids to gene name/description?
fastq annotation genomics rnaseq
3.6 years ago by O.rka ▴ 750
0
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0
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1.4k
views
Comment: Comment: Where can I find an annotation table for human gencode ensemble gene ids to gene
3.6 years ago by O.rka ▴ 750
3
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4
replies
1.7k
views
What are some good uses of [sorted].bam files after RNA-seq?
genomics rnaseq fastq
updated 3.7 years ago by 45k • written 3.7 years ago by ▴ 750
0
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1
reply
11k
views
Comment: Comment: featureCounts isoform vs gene summarization
3.7 years ago by O.rka ▴ 750
0
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0
replies
560
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How do you use ERCC spike-ins for ALR Transformation of RNA-seq data?
fastq genomics rnaseq
3.7 years ago by O.rka ▴ 750
0
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0
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643
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How to find "consensus classification" for a cluster of highly similar metagenome assembled genomes [MAG]?
metatranscriptomics classification binning metagenomics
3.7 years ago by O.rka ▴ 750
0
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1
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1.7k
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Comment: Comment: Any alternatives to BBMap's clumpify.sh program to optimize gzip compression?
3.7 years ago by O.rka ▴ 750
0
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1
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1.7k
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Comment: Comment: Any alternatives to BBMap's clumpify.sh program to optimize gzip compression?
3.7 years ago by O.rka ▴ 750
1
vote
6
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1.7k
views
Any alternatives to BBMap's clumpify.sh program to optimize gzip compression?
fastq genomics rnaseq
updated 3.7 years ago by 153k • written 3.7 years ago by ▴ 750
1
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1
reply
1.8k
views
Comment: Comment: How to get consensus annotations for a de novo orthogroup/ortholog analysis?
3.8 years ago by O.rka ▴ 750
1
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1
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1.8k
views
Comment: Comment: How to get consensus annotations for a de novo orthogroup/ortholog analysis?
3.8 years ago by O.rka ▴ 750
3
votes
5
replies
1.8k
views
How to get consensus annotations for a de novo orthogroup/ortholog analysis?
metatranscriptomics metagenomics transcriptomics
updated 3.8 years ago by ★ 2.9k • written 3.8 years ago by ▴ 750
0
votes
0
replies
983
views
Comment: Comment: How can I test whether a treatment truncates transcript length using transcripto
3.8 years ago by O.rka ▴ 750
0
votes
2
replies
983
views
How can I test whether a treatment truncates transcript length using transcriptomics?
genomics transcriptomics statistics
3.8 years ago by O.rka ▴ 750
0
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0
replies
1.6k
views
Comment: Comment: How to download BBTools sketch databases using fetchRefSeq?
3.9 years ago by O.rka ▴ 750
0
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0
replies
622
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
3.9 years ago by O.rka ▴ 750
0
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1
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1.6k
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Comment: Comment: How to download BBTools sketch databases using fetchRefSeq?
3.9 years ago by O.rka ▴ 750
0
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4
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1.6k
views
How to download BBTools sketch databases using fetchRefSeq?
metagenomics bbmap sketch bbtools
3.9 years ago by O.rka ▴ 750
0
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1
reply
17k
views
Comment: Comment: BBSketch - A Tool for Rapid Sequence Comparison
3.9 years ago by O.rka ▴ 750
1
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1
reply
3.3k
views
How to merge HMM files for HMMSearch?
alignment hmm protein annotation
updated 3.9 years ago by ★ 30k • written 3.9 years ago by ▴ 750
0
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0
replies
671
views
Any ORF callers that have an option to choose first N ORFs?
metagenomics genomics metatranscriptomics
4.0 years ago by O.rka ▴ 750
1
vote
4
replies
1.7k
views
How to adapt a for loop of `muscle` alignments using GNU Parallel?
alignment bash parallel
4.0 years ago by O.rka ▴ 750
1
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0
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1.7k
views
Answer: Answer: How to adapt a for loop of `muscle` alignments using GNU Parallel?
4.0 years ago by O.rka ▴ 750
0
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0
replies
2.7k
views
Comment: Comment: Recommended approach for building phylogenetic tree from de novo metagenomes
4.0 years ago by O.rka ▴ 750
0
votes
0
replies
18k
views
Comment: Comment: How To Add Specific Word To Fasta Header
4.0 years ago by O.rka ▴ 750
1
vote
4
replies
2.7k
views
Recommended approach for building phylogenetic tree from de novo metagenomes
phylogenetic tree Metagenomics
4.0 years ago by O.rka ▴ 750
0
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0
replies
2.7k
views
Comment: Comment: Recommended approach for building phylogenetic tree from de novo metagenomes
4.0 years ago by O.rka ▴ 750
4
votes
2
replies
2.4k
views
What is the recommended way to subsample Oxford Nanopore (ONT) fastq reads with matching fast5?
sequencing
4.0 years ago by O.rka ▴ 750
2
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0
replies
2.4k
views
Answer: Answer: What is the recommended way to subsample Oxford Nanopore (ONT) fastq reads with
4.0 years ago by O.rka ▴ 750
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