Profile Posts Awards
Show
all questions tools blogs news tutorials forum answers comments
2
votes
1
reply
439
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
9 weeks ago by O.rka ▴ 740
0
votes
0
replies
226
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition kegg module database genomics
3 months ago by O.rka ▴ 740
0
votes
0
replies
232
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics metacyc enzyme pathway genomics
4 months ago by O.rka ▴ 740
0
votes
1
reply
583
views
Comment: Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
4 months ago by O.rka ▴ 740
1
vote
3
replies
583
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 4 months ago by ★ 28k • written 4 months ago by ▴ 740
0
votes
0
replies
442
views
Comment: Comment: Help with understanding the identifier mapping tables in the backend of HUMAnN
4 months ago by O.rka ▴ 740
0
votes
2
replies
442
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics metacyc enzyme biobakery humann
4 months ago by O.rka ▴ 740
0
votes
0
replies
487
views
Comment: Comment: Why are gene models from JGI non-sense when using AGAT to to extract proteins?
5 months ago by O.rka ▴ 740
0
votes
2
replies
487
views
Why are gene models from JGI non-sense when using AGAT to to extract proteins?
translation models gif gene cgi
5 months ago by O.rka ▴ 740
1
vote
1
reply
650
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 6 months ago by ▴ 10 • written 9 months ago by ▴ 740
0
votes
1
reply
649
views
How can I calculate the percent of bases covered in the query assembly relative to the reference assembly?
samtools
updated 7 months ago by ★ 2.4k • written 7 months ago by ▴ 740
0
votes
0
replies
857
views
Comment: Comment: How to use Nextflow to call scripts from different environments?
8 months ago by O.rka ▴ 740
1
vote
2
replies
857
views
How to use Nextflow to call scripts from different environments?
anaconda conda nextflow
8 months ago by O.rka ▴ 740
2
votes
1
reply
663
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam sam reads fastq
updated 9 months ago by 13k • written 9 months ago by ▴ 740
2
votes
3
replies
896
views
How to check if my sequence is DNA or Protein in BioPython?
genomics biopython fasta
updated 9 months ago by 21k • written 9 months ago by ▴ 740
1
vote
1
reply
710
views
How to download taxonomy/lineage/taxonid information for JGI genome organism codes? (e.g., MycoCosm and PhycoCosm)
jgi genomics phycocosm mycocosm taxonomy
10 months ago by O.rka ▴ 740
1
vote
0
replies
710
views
Answer: Answer: How to download taxonomy/lineage/taxonid information for JGI genome organism co
10 months ago by O.rka ▴ 740
0
votes
0
replies
687
views
Comment: Comment: Why are some HUMAnN features in [name]_pathabundance.tsv missing taxonomy?
10 months ago by O.rka ▴ 740
0
votes
2
replies
687
views
Why are some HUMAnN features in [name]_pathabundance.tsv missing taxonomy?
metagenomics metabolism humann biobakery metatranscriptomics
10 months ago by O.rka ▴ 740
0
votes
1
reply
579
views
How to download genomes and proteins from JGI in bulk via the command line?
jgi cli
updated 11 months ago by 44k • written 11 months ago by ▴ 740
1
vote
3
replies
826
views
How to convert between UniRef50 to EC/enzyme number?
Uniref conversion uniprot enzyme
updated 11 months ago by ★ 2.4k • written 11 months ago by ▴ 740
0
votes
0
replies
826
views
Comment: Comment: How to convert between UniRef50 to EC/enzyme number?
11 months ago by O.rka ▴ 740
0
votes
0
replies
859
views
Comment: Comment: How to run TRUST4 for BCR/TCR detection using 10X data?
11 months ago by O.rka ▴ 740
0
votes
2
replies
859
views
How to run TRUST4 for BCR/TCR detection using 10X data?
immunology trust4 illumina 10x
11 months ago by O.rka ▴ 740
7
votes
9
replies
2.1k
views
6 follow
How can I transfer gene models to a new assembly?
gene Assembly
updated 12 months ago by 8.7k • written 4.4 years ago by ▴ 740
0
votes
1
reply
963
views
Comment: Comment: When counting ASVs in DADA2, does a hit/count only occur at 100% alignment perce
12 months ago by O.rka ▴ 740
0
votes
1
reply
2.1k
views
Answer: Answer: How can I transfer gene models to a new assembly?
12 months ago by O.rka ▴ 740
3
votes
3
replies
963
views
When counting ASVs in DADA2, does a hit/count only occur at 100% alignment percent identity?
metagenomics qiime2 amplicon 16s dada2
updated 12 months ago by 3.7k • written 12 months ago by ▴ 740
0
votes
0
replies
408
views
What criteria are used to determine significant HMMER hits?
kegg protein kofamscan annotation metagenomics
13 months ago by O.rka ▴ 740
0
votes
1
reply
715
views
Using tRNAscan-SE for mitochondria tRNA from microeukaryotes like protists and yeast?
trnascan yeasts eukaryotes protists trna
updated 14 months ago by ★ 1.3k • written 14 months ago by ▴ 740
3
votes
2
replies
2.4k
views
Help speeding up HMMER's HMMSearch algorithm for large fasta file with GNU Parallel
protein parallel hmmer hmm bash
updated 14 months ago by 15k • written 3.1 years ago by ▴ 740
0
votes
1
reply
2.0k
views
Comment: Comment: How can I speed up wget from UniProt for UniRef90/50 fasta?
15 months ago by O.rka ▴ 740
0
votes
1
reply
2.0k
views
Comment: Comment: How can I speed up wget from UniProt for UniRef90/50 fasta?
15 months ago by O.rka ▴ 740
0
votes
1
reply
2.0k
views
Comment: Comment: How can I speed up wget from UniProt for UniRef90/50 fasta?
15 months ago by O.rka ▴ 740
0
votes
7
replies
2.0k
views
How can I speed up wget from UniProt for UniRef90/50 fasta?
wget download uniprot uniref
updated 15 months ago by ★ 28k • written 15 months ago by ▴ 740
0
votes
0
replies
25k
views
Comment: Comment: Variant call format (VCF) file, how to get statistics per sample?
16 months ago by O.rka ▴ 740
0
votes
0
replies
1.4k
views
Comment: Comment: Should you specify "-p" for paired end reads using featureCounts?
16 months ago by O.rka ▴ 740
0
votes
1
reply
1.4k
views
Comment: Comment: Should you specify "-p" for paired end reads using featureCounts?
16 months ago by O.rka ▴ 740
4
votes
6
replies
1.4k
views
Should you specify "-p" for paired end reads using featureCounts?
fastq rnaseq genomics
16 months ago by O.rka ▴ 740
0
votes
0
replies
344
views
How can I get taxa relative abundances from HUMAnN?
metagenomics humann biobakery metatranscriptomics
16 months ago by O.rka ▴ 740
0
votes
0
replies
2.6k
views
Comment: Comment: Most efficient way to run Diamond against a very very large database (i.e., NCBI
17 months ago by O.rka ▴ 740
0
votes
1
reply
2.6k
views
Comment: Comment: Most efficient way to run Diamond against a very very large database (i.e., NCBI
17 months ago by O.rka ▴ 740
5
votes
9
replies
2.6k
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 12 months ago by 145k • written 17 months ago by ▴ 740
0
votes
1
reply
1.0k
views
Comment: Comment: How can I determine the number of detected genes and detected transcripts/isofor
17 months ago by O.rka ▴ 740
0
votes
1
reply
1.0k
views
Comment: Comment: How can I determine the number of detected genes and detected transcripts/isofor
17 months ago by O.rka ▴ 740
0
votes
5
replies
1.0k
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 17 months ago by 145k • written 17 months ago by ▴ 740
0
votes
0
replies
394
views
Why did I get more unique genes than unique transcripts w/ STAR -> featureCounts?
rnaseq genomics star fastq alignment
17 months ago by O.rka ▴ 740
0
votes
1
reply
1.4k
views
Comment: Comment: How do you download from CyVerse using FTP or wget?
17 months ago by O.rka ▴ 740
0
votes
2
replies
1.4k
views
Comment: Comment: How do you download from CyVerse using FTP or wget?
17 months ago by O.rka ▴ 740
8
votes
6
replies
1.4k
views
How do you download from CyVerse using FTP or wget?
cyverse
updated 17 months ago by 44k • written 17 months ago by ▴ 740
410 results • Page 1 of 9
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6