This is a test version of Biostars. For the public version, visit https://www.biostars.org.
O.rka
O.rka
Reputation:
750 (Trusted)
Joined:
10.4 years ago
Last seen:
2.2 years ago
Location:
Chula Vista
Latest posts by user
2 votes
1 reply
2.4K views
Tool: Just released VEBA 2.0 in Nucleic Acids Research, a modular genome-resolved metagenomics/metatranscriptomics software suite that can handle prokaryotes, (micro)eukaryotes, and viruses
metatranscriptomics metagenomics microbiome veba
written by O.rka 75
0 votes
0 replies
763 views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition kegg module database genomics
written by O.rka 75
0 votes
0 replies
648 views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics metacyc enzyme pathway genomics
written by O.rka 75
0 votes
1 reply
0 views
Comment: Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
written by O.rka 75
0 votes
3 replies
1.8K 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 by Mensur Dlakic 3.0K • | written by O.rka 75
0 votes
0 replies
0 views
Comment: Comment: Help with understanding the identifier mapping tables in the backend of HUMAnN
written by O.rka 75
0 votes
2 replies
1.4K views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics metacyc enzyme biobakery humann
written by O.rka 75
0 votes
0 replies
0 views
Comment: Comment: Why are gene models from JGI non-sense when using AGAT to to extract proteins?
written by O.rka 75
0 votes
2 replies
1.4K views
Why are gene models from JGI non-sense when using AGAT to to extract proteins?
translation models gif gene cgi
written by O.rka 75
0 votes
1 reply
1.1K views
How can I calculate the percent of bases covered in the query assembly relative to the reference assembly?
samtools
updated by dthorbur 350 • | written by O.rka 75
0 votes
0 replies
0 views
Comment: Comment: How to use Nextflow to call scripts from different environments?
written by O.rka 75
0 votes
2 replies
1.9K views
How to use Nextflow to call scripts from different environments?
anaconda conda nextflow
written by O.rka 75
0 votes
1 reply
1.4K 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 by akshay 1 • | written by O.rka 75
0 votes
1 reply
1.8K views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam sam reads fastq
updated by rpolicastro 1.3K • | written by O.rka 75
0 votes
3 replies
2.1K views
How to check if my sequence is DNA or Protein in BioPython?
genomics biopython fasta
updated by Joe 2.2K • | written by O.rka 75
1 vote
0 replies
0 views
Answer: Answer: How to download taxonomy/lineage/taxonid information for JGI genome organism co
written by O.rka 75
0 votes
1 reply
1.4K views
How to download taxonomy/lineage/taxonid information for JGI genome organism codes? (e.g., MycoCosm and PhycoCosm)
jgi genomics phycocosm mycocosm taxonomy
written by O.rka 75
0 votes
0 replies
0 views
Comment: Comment: Why are some HUMAnN features in [name]_pathabundance.tsv missing taxonomy?
written by O.rka 75
0 votes
2 replies
1.7K views
Why are some HUMAnN features in [name]_pathabundance.tsv missing taxonomy?
metagenomics metabolism humann biobakery metatranscriptomics
written by O.rka 75
0 votes
1 reply
1.6K views
How to download genomes and proteins from JGI in bulk via the command line?
jgi cli
updated by Ram 4.5K • | written by O.rka 75
Latest awards to user
TODO: Awards