Profile Posts Awards
Show
all questions tools blogs news tutorials forum answers comments
Showing : all
0
votes
0
replies
142
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics metacyc enzyme pathway genomics
5 days ago by O.rka ▴ 710
0
votes
1
reply
398
views
Comment: Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
8 days ago by O.rka ▴ 710
1
vote
3
replies
398
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 7 days ago by ★ 27k • written 9 days ago by ▴ 710
0
votes
0
replies
335
views
Comment: Comment: Help with understanding the identifier mapping tables in the backend of HUMAnN
22 days ago by O.rka ▴ 710
0
votes
2
replies
335
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics metacyc enzyme biobakery humann
22 days ago by O.rka ▴ 710
0
votes
0
replies
345
views
Comment: Comment: Why are gene models from JGI non-sense when using AGAT to to extract proteins?
4 weeks ago by O.rka ▴ 710
0
votes
2
replies
345
views
Why are gene models from JGI non-sense when using AGAT to to extract proteins?
translation models gif gene cgi
4 weeks ago by O.rka ▴ 710
1
vote
1
reply
509
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 10 weeks ago by ▴ 10 • written 5 months ago by ▴ 710
0
votes
1
reply
574
views
How can I calculate the percent of bases covered in the query assembly relative to the reference assembly?
samtools
updated 3 months ago by ★ 1.9k • written 3 months ago by ▴ 710
0
votes
0
replies
666
views
Comment: Comment: How to use Nextflow to call scripts from different environments?
4 months ago by O.rka ▴ 710
1
vote
2
replies
666
views
How to use Nextflow to call scripts from different environments?
anaconda conda nextflow
4 months ago by O.rka ▴ 710
2
votes
1
reply
476
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam sam reads fastq
updated 5 months ago by 13k • written 5 months ago by ▴ 710
2
votes
3
replies
720
views
How to check if my sequence is DNA or Protein in BioPython?
genomics biopython fasta
updated 5 months ago by 21k • written 5 months ago by ▴ 710
1
vote
1
reply
616
views
How to download taxonomy/lineage/taxonid information for JGI genome organism codes? (e.g., MycoCosm and PhycoCosm)
jgi genomics phycocosm mycocosm taxonomy
6 months ago by O.rka ▴ 710
1
vote
0
replies
616
views
Answer: Answer: How to download taxonomy/lineage/taxonid information for JGI genome organism co
6 months ago by O.rka ▴ 710
0
votes
0
replies
559
views
Comment: Comment: Why are some HUMAnN features in [name]_pathabundance.tsv missing taxonomy?
6 months ago by O.rka ▴ 710
0
votes
2
replies
559
views
Why are some HUMAnN features in [name]_pathabundance.tsv missing taxonomy?
metagenomics metabolism humann biobakery metatranscriptomics
6 months ago by O.rka ▴ 710
0
votes
1
reply
462
views
How to download genomes and proteins from JGI in bulk via the command line?
jgi cli
updated 7 months ago by 43k • written 7 months ago by ▴ 710
1
vote
3
replies
682
views
How to convert between UniRef50 to EC/enzyme number?
Uniref conversion uniprot enzyme
updated 7 months ago by ★ 2.4k • written 7 months ago by ▴ 710
0
votes
0
replies
682
views
Comment: Comment: How to convert between UniRef50 to EC/enzyme number?
7 months ago by O.rka ▴ 710
0
votes
0
replies
692
views
Comment: Comment: How to run TRUST4 for BCR/TCR detection using 10X data?
7 months ago by O.rka ▴ 710
0
votes
2
replies
692
views
How to run TRUST4 for BCR/TCR detection using 10X data?
immunology trust4 illumina 10x
7 months ago by O.rka ▴ 710
7
votes
9
replies
1.9k
views
6 follow
How can I transfer gene models to a new assembly?
gene Assembly
updated 8 months ago by 8.4k • written 4.1 years ago by ▴ 710
0
votes
1
reply
807
views
Comment: Comment: When counting ASVs in DADA2, does a hit/count only occur at 100% alignment perce
8 months ago by O.rka ▴ 710
0
votes
1
reply
1.9k
views
Answer: Answer: How can I transfer gene models to a new assembly?
8 months ago by O.rka ▴ 710
3
votes
3
replies
807
views
When counting ASVs in DADA2, does a hit/count only occur at 100% alignment percent identity?
metagenomics qiime2 amplicon 16s dada2
updated 8 months ago by 3.6k • written 8 months ago by ▴ 710
0
votes
0
replies
354
views
What criteria are used to determine significant HMMER hits?
kegg protein kofamscan annotation metagenomics
9 months ago by O.rka ▴ 710
0
votes
1
reply
606
views
Using tRNAscan-SE for mitochondria tRNA from microeukaryotes like protists and yeast?
trnascan yeasts eukaryotes protists trna
updated 10 months ago by ★ 1.2k • written 10 months ago by ▴ 710
3
votes
2
replies
2.1k
views
Help speeding up HMMER's HMMSearch algorithm for large fasta file with GNU Parallel
protein parallel hmmer hmm bash
updated 10 months ago by 15k • written 2.7 years ago by ▴ 710
0
votes
1
reply
1.7k
views
Comment: Comment: How can I speed up wget from UniProt for UniRef90/50 fasta?
11 months ago by O.rka ▴ 710
0
votes
1
reply
1.7k
views
Comment: Comment: How can I speed up wget from UniProt for UniRef90/50 fasta?
11 months ago by O.rka ▴ 710
0
votes
1
reply
1.7k
views
Comment: Comment: How can I speed up wget from UniProt for UniRef90/50 fasta?
11 months ago by O.rka ▴ 710
0
votes
7
replies
1.7k
views
How can I speed up wget from UniProt for UniRef90/50 fasta?
wget download uniprot uniref
updated 11 months ago by ★ 27k • written 11 months ago by ▴ 710
0
votes
0
replies
24k
views
Comment: Comment: Variant call format (VCF) file, how to get statistics per sample?
12 months ago by O.rka ▴ 710
0
votes
0
replies
1.2k
views
Comment: Comment: Should you specify "-p" for paired end reads using featureCounts?
12 months ago by O.rka ▴ 710
0
votes
1
reply
1.2k
views
Comment: Comment: Should you specify "-p" for paired end reads using featureCounts?
12 months ago by O.rka ▴ 710
4
votes
6
replies
1.2k
views
Should you specify "-p" for paired end reads using featureCounts?
fastq rnaseq genomics
12 months ago by O.rka ▴ 710
0
votes
0
replies
292
views
How can I get taxa relative abundances from HUMAnN?
metagenomics humann biobakery metatranscriptomics
13 months ago by O.rka ▴ 710
0
votes
0
replies
2.1k
views
Comment: Comment: Most efficient way to run Diamond against a very very large database (i.e., NCBI
13 months ago by O.rka ▴ 710
0
votes
1
reply
2.1k
views
Comment: Comment: Most efficient way to run Diamond against a very very large database (i.e., NCBI
13 months ago by O.rka ▴ 710
5
votes
9
replies
2.1k
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 9 months ago by 142k • written 13 months ago by ▴ 710
0
votes
1
reply
903
views
Comment: Comment: How can I determine the number of detected genes and detected transcripts/isofor
13 months ago by O.rka ▴ 710
0
votes
1
reply
903
views
Comment: Comment: How can I determine the number of detected genes and detected transcripts/isofor
13 months ago by O.rka ▴ 710
0
votes
5
replies
903
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 13 months ago by 142k • written 13 months ago by ▴ 710
0
votes
0
replies
352
views
Why did I get more unique genes than unique transcripts w/ STAR -> featureCounts?
rnaseq genomics star fastq alignment
13 months ago by O.rka ▴ 710
0
votes
1
reply
1.2k
views
Comment: Comment: How do you download from CyVerse using FTP or wget?
13 months ago by O.rka ▴ 710
0
votes
2
replies
1.2k
views
Comment: Comment: How do you download from CyVerse using FTP or wget?
13 months ago by O.rka ▴ 710
8
votes
6
replies
1.2k
views
How do you download from CyVerse using FTP or wget?
cyverse
updated 13 months ago by 43k • written 13 months ago by ▴ 710
3
votes
3
replies
2.2k
views
How to fix "Please indicate the file directory in 'setting' file?" for MaxBin2?
maxbin2 binning metagenomics
updated 12 months ago by 43k • written 2.9 years ago by ▴ 710
0
votes
0
replies
735
views
Comment: Comment: t2t human reference genome for RNA-seq
14 months ago by O.rka ▴ 710
408 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