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633
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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
5 months ago by O.rka ▴ 740
0
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0
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270
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Help interpreting KEGG module definitions for converting to NetworkX graph
definition kegg module database genomics
6 months ago by O.rka ▴ 740
0
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0
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268
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What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics metacyc enzyme pathway genomics
7 months ago by O.rka ▴ 740
0
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1
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687
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Comment: Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
7 months ago by O.rka ▴ 740
1
vote
3
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687
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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 months ago by ★ 28k • written 7 months ago by ▴ 740
0
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0
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504
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Comment: Comment: Help with understanding the identifier mapping tables in the backend of HUMAnN
7 months ago by O.rka ▴ 740
0
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2
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504
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Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics metacyc enzyme biobakery humann
7 months ago by O.rka ▴ 740
0
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0
replies
569
views
Comment: Comment: Why are gene models from JGI non-sense when using AGAT to to extract proteins?
8 months ago by O.rka ▴ 740
0
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2
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569
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Why are gene models from JGI non-sense when using AGAT to to extract proteins?
translation models gif gene cgi
8 months ago by O.rka ▴ 740
1
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1
reply
721
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 9 months ago by ▴ 10 • written 12 months ago by ▴ 740
0
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1
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685
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How can I calculate the percent of bases covered in the query assembly relative to the reference assembly?
samtools
updated 10 months ago by ★ 2.5k • written 10 months ago by ▴ 740
0
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0
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961
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Comment: Comment: How to use Nextflow to call scripts from different environments?
11 months ago by O.rka ▴ 740
1
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2
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961
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How to use Nextflow to call scripts from different environments?
anaconda conda nextflow
11 months ago by O.rka ▴ 740
2
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1
reply
773
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam sam reads fastq
updated 12 months ago by 13k • written 12 months ago by ▴ 740
2
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3
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999
views
How to check if my sequence is DNA or Protein in BioPython?
genomics biopython fasta
updated 12 months ago by 21k • written 12 months ago by ▴ 740
1
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1
reply
759
views
How to download taxonomy/lineage/taxonid information for JGI genome organism codes? (e.g., MycoCosm and PhycoCosm)
jgi genomics phycocosm mycocosm taxonomy
13 months ago by O.rka ▴ 740
1
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0
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759
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Answer: Answer: How to download taxonomy/lineage/taxonid information for JGI genome organism co
13 months ago by O.rka ▴ 740
0
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0
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761
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Comment: Comment: Why are some HUMAnN features in [name]_pathabundance.tsv missing taxonomy?
13 months ago by O.rka ▴ 740
0
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2
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761
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Why are some HUMAnN features in [name]_pathabundance.tsv missing taxonomy?
metagenomics metabolism humann biobakery metatranscriptomics
13 months ago by O.rka ▴ 740
0
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1
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681
views
How to download genomes and proteins from JGI in bulk via the command line?
jgi cli
updated 14 months ago by 44k • written 14 months ago by ▴ 740
1
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3
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906
views
How to convert between UniRef50 to EC/enzyme number?
Uniref conversion uniprot enzyme
updated 14 months ago by ★ 2.4k • written 14 months ago by ▴ 740
0
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0
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906
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Comment: Comment: How to convert between UniRef50 to EC/enzyme number?
14 months ago by O.rka ▴ 740
0
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0
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971
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Comment: Comment: How to run TRUST4 for BCR/TCR detection using 10X data?
14 months ago by O.rka ▴ 740
0
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2
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971
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How to run TRUST4 for BCR/TCR detection using 10X data?
immunology trust4 illumina 10x
14 months ago by O.rka ▴ 740
7
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9
replies
2.2k
views
6 follow
How can I transfer gene models to a new assembly?
gene Assembly
updated 15 months ago by 8.8k • written 4.7 years ago by ▴ 740
0
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1
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1.0k
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Comment: Comment: When counting ASVs in DADA2, does a hit/count only occur at 100% alignment perce
15 months ago by O.rka ▴ 740
0
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1
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2.2k
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Answer: Answer: How can I transfer gene models to a new assembly?
15 months ago by O.rka ▴ 740
3
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3
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1.0k
views
When counting ASVs in DADA2, does a hit/count only occur at 100% alignment percent identity?
metagenomics qiime2 amplicon 16s dada2
updated 15 months ago by 3.8k • written 15 months ago by ▴ 740
0
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0
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431
views
What criteria are used to determine significant HMMER hits?
kegg protein kofamscan annotation metagenomics
16 months ago by O.rka ▴ 740
0
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1
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765
views
Using tRNAscan-SE for mitochondria tRNA from microeukaryotes like protists and yeast?
trnascan yeasts eukaryotes protists trna
updated 17 months ago by ★ 1.4k • written 17 months ago by ▴ 740
3
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2
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2.7k
views
Help speeding up HMMER's HMMSearch algorithm for large fasta file with GNU Parallel
protein parallel hmmer hmm bash
updated 17 months ago by 15k • written 3.3 years ago by ▴ 740
0
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1
reply
2.2k
views
Comment: Comment: How can I speed up wget from UniProt for UniRef90/50 fasta?
18 months ago by O.rka ▴ 740
0
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1
reply
2.2k
views
Comment: Comment: How can I speed up wget from UniProt for UniRef90/50 fasta?
18 months ago by O.rka ▴ 740
0
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1
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2.2k
views
Comment: Comment: How can I speed up wget from UniProt for UniRef90/50 fasta?
18 months ago by O.rka ▴ 740
0
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7
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2.2k
views
How can I speed up wget from UniProt for UniRef90/50 fasta?
wget download uniprot uniref
updated 18 months ago by ★ 28k • written 18 months ago by ▴ 740
0
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0
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26k
views
Comment: Comment: Variant call format (VCF) file, how to get statistics per sample?
19 months ago by O.rka ▴ 740
0
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0
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1.5k
views
Comment: Comment: Should you specify "-p" for paired end reads using featureCounts?
19 months ago by O.rka ▴ 740
0
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1
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1.5k
views
Comment: Comment: Should you specify "-p" for paired end reads using featureCounts?
19 months ago by O.rka ▴ 740
4
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6
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1.5k
views
Should you specify "-p" for paired end reads using featureCounts?
fastq rnaseq genomics
19 months ago by O.rka ▴ 740
0
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0
replies
372
views
How can I get taxa relative abundances from HUMAnN?
metagenomics humann biobakery metatranscriptomics
20 months ago by O.rka ▴ 740
0
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0
replies
2.9k
views
Comment: Comment: Most efficient way to run Diamond against a very very large database (i.e., NCBI
20 months ago by O.rka ▴ 740
0
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1
reply
2.9k
views
Comment: Comment: Most efficient way to run Diamond against a very very large database (i.e., NCBI
20 months ago by O.rka ▴ 740
5
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9
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2.9k
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 16 months ago by 147k • written 20 months ago by ▴ 740
0
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1
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1.1k
views
Comment: Comment: How can I determine the number of detected genes and detected transcripts/isofor
20 months ago by O.rka ▴ 740
0
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1
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1.1k
views
Comment: Comment: How can I determine the number of detected genes and detected transcripts/isofor
20 months ago by O.rka ▴ 740
0
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5
replies
1.1k
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 20 months ago by 147k • written 20 months ago by ▴ 740
0
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0
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417
views
Why did I get more unique genes than unique transcripts w/ STAR -> featureCounts?
rnaseq genomics star fastq alignment
20 months ago by O.rka ▴ 740
0
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1
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1.5k
views
Comment: Comment: How do you download from CyVerse using FTP or wget?
20 months ago by O.rka ▴ 740
0
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2
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1.5k
views
Comment: Comment: How do you download from CyVerse using FTP or wget?
20 months ago by O.rka ▴ 740
8
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6
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1.5k
views
How do you download from CyVerse using FTP or wget?
cyverse
updated 20 months ago by 44k • written 20 months ago by ▴ 740
410 results • Page 1 of 9
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