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3
votes
5
replies
9.5k
views
6 follow
How to fix "Please indicate the file directory in 'setting' file?" for MaxBin2?
maxbin2 binning metagenomics
updated 7 weeks ago by 154k • written 4.4 years ago by ▴ 750
2
votes
1
reply
2.0k
views
Tool: Just released VEBA 2.0 in Nucleic Acids Research, a modular genome-resolved metagenomics/metatranscriptomics software suite that can handle prokaryot…
metatranscriptomics metagenomics microbiome veba
16 months ago by O.rka ▴ 750
0
votes
0
replies
524
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition kegg module database genomics
17 months ago by O.rka ▴ 750
0
votes
0
replies
470
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics metacyc enzyme pathway genomics
18 months ago by O.rka ▴ 750
0
votes
1
reply
1.3k
views
Comment: Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
18 months ago by O.rka ▴ 750
1
vote
3
replies
1.3k
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology metagenomics database enzymes genomics
updated 18 months ago by ★ 30k • written 18 months ago by ▴ 750
0
votes
0
replies
1.0k
views
Comment: Comment: Help with understanding the identifier mapping tables in the backend of HUMAnN
18 months ago by O.rka ▴ 750
0
votes
2
replies
1.0k
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics metacyc enzyme biobakery humann
18 months ago by O.rka ▴ 750
0
votes
0
replies
1.1k
views
Comment: Comment: Why are gene models from JGI non-sense when using AGAT to to extract proteins?
19 months ago by O.rka ▴ 750
0
votes
2
replies
1.1k
views
Why are gene models from JGI non-sense when using AGAT to to extract proteins?
translation models gif gene cgi
19 months ago by O.rka ▴ 750
1
vote
1
reply
1.1k
views
How to estimate -g genome-size for Flye for de novo genome or for --meta mode when using Metaflye?
assembly fasta genomics nanopore pacbio
updated 20 months ago by ▴ 10 • written 23 months ago by ▴ 750
0
votes
1
reply
914
views
How can I calculate the percent of bases covered in the query assembly relative to the reference assembly?
samtools
updated 21 months ago by ★ 3.1k • written 21 months ago by ▴ 750
0
votes
0
replies
1.6k
views
Comment: Comment: How to use Nextflow to call scripts from different environments?
23 months ago by O.rka ▴ 750
1
vote
2
replies
1.6k
views
How to use Nextflow to call scripts from different environments?
anaconda conda nextflow
23 months ago by O.rka ▴ 750
2
votes
1
reply
1.4k
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam sam reads fastq
updated 23 months ago by 13k • written 23 months ago by ▴ 750
2
votes
3
replies
1.6k
views
How to check if my sequence is DNA or Protein in BioPython?
genomics biopython fasta
updated 23 months ago by 22k • written 24 months ago by ▴ 750
1
vote
1
reply
1.2k
views
How to download taxonomy/lineage/taxonid information for JGI genome organism codes? (e.g., MycoCosm and PhycoCosm)
jgi genomics phycocosm mycocosm taxonomy
2.0 years ago by O.rka ▴ 750
1
vote
0
replies
1.2k
views
Answer: Answer: How to download taxonomy/lineage/taxonid information for JGI genome organism co
2.0 years ago by O.rka ▴ 750
0
votes
0
replies
1.3k
views
Comment: Comment: Why are some HUMAnN features in [name]_pathabundance.tsv missing taxonomy?
2.1 years ago by O.rka ▴ 750
0
votes
2
replies
1.3k
views
Why are some HUMAnN features in [name]_pathabundance.tsv missing taxonomy?
metagenomics metabolism humann biobakery metatranscriptomics
2.1 years ago by O.rka ▴ 750
0
votes
1
reply
1.2k
views
How to download genomes and proteins from JGI in bulk via the command line?
jgi cli
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 750
1
vote
3
replies
1.5k
views
How to convert between UniRef50 to EC/enzyme number?
Uniref conversion uniprot enzyme
updated 2.1 years ago by ★ 2.4k • written 2.1 years ago by ▴ 750
0
votes
0
replies
1.5k
views
Comment: Comment: How to convert between UniRef50 to EC/enzyme number?
2.1 years ago by O.rka ▴ 750
0
votes
0
replies
1.6k
views
Comment: Comment: How to run TRUST4 for BCR/TCR detection using 10X data?
2.1 years ago by O.rka ▴ 750
0
votes
2
replies
1.6k
views
How to run TRUST4 for BCR/TCR detection using 10X data?
immunology trust4 illumina 10x
2.1 years ago by O.rka ▴ 750
7
votes
9
replies
3.1k
views
6 follow
How can I transfer gene models to a new assembly?
gene Assembly
updated 2.2 years ago by 8.9k • written 5.6 years ago by ▴ 750
0
votes
1
reply
1.6k
views
Comment: Comment: When counting ASVs in DADA2, does a hit/count only occur at 100% alignment perce
2.2 years ago by O.rka ▴ 750
0
votes
1
reply
3.1k
views
Answer: Answer: How can I transfer gene models to a new assembly?
2.2 years ago by O.rka ▴ 750
3
votes
3
replies
1.6k
views
When counting ASVs in DADA2, does a hit/count only occur at 100% alignment percent identity?
metagenomics qiime2 amplicon 16s dada2
updated 2.2 years ago by 3.9k • written 2.2 years ago by ▴ 750
0
votes
0
replies
631
views
What criteria are used to determine significant HMMER hits?
kegg protein kofamscan annotation metagenomics
2.3 years ago by O.rka ▴ 750
0
votes
1
reply
1.1k
views
Using tRNAscan-SE for mitochondria tRNA from microeukaryotes like protists and yeast?
trnascan yeasts eukaryotes protists trna
updated 2.4 years ago by ★ 1.8k • written 2.4 years ago by ▴ 750
3
votes
2
replies
3.9k
views
Help speeding up HMMER's HMMSearch algorithm for large fasta file with GNU Parallel
protein parallel hmmer hmm bash
updated 2.4 years ago by 16k • written 4.2 years ago by ▴ 750
0
votes
1
reply
3.3k
views
Comment: Comment: How can I speed up wget from UniProt for UniRef90/50 fasta?
2.5 years ago by O.rka ▴ 750
0
votes
1
reply
3.3k
views
Comment: Comment: How can I speed up wget from UniProt for UniRef90/50 fasta?
2.5 years ago by O.rka ▴ 750
0
votes
1
reply
3.3k
views
Comment: Comment: How can I speed up wget from UniProt for UniRef90/50 fasta?
2.5 years ago by O.rka ▴ 750
0
votes
7
replies
3.3k
views
How can I speed up wget from UniProt for UniRef90/50 fasta?
wget download uniprot uniref
updated 2.5 years ago by ★ 30k • written 2.5 years ago by ▴ 750
0
votes
0
replies
27k
views
Comment: Comment: Variant call format (VCF) file, how to get statistics per sample?
2.5 years ago by O.rka ▴ 750
0
votes
0
replies
2.3k
views
Comment: Comment: Should you specify "-p" for paired end reads using featureCounts?
2.5 years ago by O.rka ▴ 750
0
votes
1
reply
2.3k
views
Comment: Comment: Should you specify "-p" for paired end reads using featureCounts?
2.5 years ago by O.rka ▴ 750
4
votes
6
replies
2.3k
views
Should you specify "-p" for paired end reads using featureCounts?
fastq rnaseq genomics
2.5 years ago by O.rka ▴ 750
0
votes
0
replies
571
views
How can I get taxa relative abundances from HUMAnN?
metagenomics humann biobakery metatranscriptomics
2.6 years ago by O.rka ▴ 750
0
votes
0
replies
4.5k
views
Comment: Comment: Most efficient way to run Diamond against a very very large database (i.e., NCBI
2.6 years ago by O.rka ▴ 750
0
votes
1
reply
4.5k
views
Comment: Comment: Most efficient way to run Diamond against a very very large database (i.e., NCBI
2.6 years ago by O.rka ▴ 750
5
votes
9
replies
4.5k
views
6 follow
Most efficient way to run Diamond against a very very large database (i.e., NCBI's NR)?
protein annotation alignment diamond nr
updated 2.2 years ago by 154k • written 2.6 years ago by ▴ 750
0
votes
1
reply
1.5k
views
Comment: Comment: How can I determine the number of detected genes and detected transcripts/isofor
2.6 years ago by O.rka ▴ 750
0
votes
1
reply
1.5k
views
Comment: Comment: How can I determine the number of detected genes and detected transcripts/isofor
2.6 years ago by O.rka ▴ 750
0
votes
5
replies
1.5k
views
How can I determine the number of detected genes and detected transcripts/isoforms in a BAM file + GTF file?
rnaseq scRNA-seq single-cell genomics ngs
updated 2.6 years ago by 154k • written 2.6 years ago by ▴ 750
0
votes
0
replies
564
views
Why did I get more unique genes than unique transcripts w/ STAR -> featureCounts?
rnaseq genomics star fastq alignment
2.6 years ago by O.rka ▴ 750
0
votes
1
reply
2.3k
views
Comment: Comment: How do you download from CyVerse using FTP or wget?
2.6 years ago by O.rka ▴ 750
0
votes
2
replies
2.3k
views
Comment: Comment: How do you download from CyVerse using FTP or wget?
2.6 years ago by O.rka ▴ 750
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