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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
10 days ago by O.rka ▴ 720
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1
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431
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Comment: Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
13 days ago by O.rka ▴ 720
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3
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431
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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 12 days ago by ★ 27k • written 14 days ago by ▴ 720
0
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0
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343
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Comment: Comment: Help with understanding the identifier mapping tables in the backend of HUMAnN
27 days ago by O.rka ▴ 720
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2
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343
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Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics metacyc enzyme biobakery humann
27 days ago by O.rka ▴ 720
0
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0
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353
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Comment: Comment: Why are gene models from JGI non-sense when using AGAT to to extract proteins?
5 weeks ago by O.rka ▴ 720
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2
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353
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Why are gene models from JGI non-sense when using AGAT to to extract proteins?
translation models gif gene cgi
5 weeks ago by O.rka ▴ 720
1
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1
reply
516
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 11 weeks ago by ▴ 10 • written 5 months ago by ▴ 720
0
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1
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580
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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 ▴ 720
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0
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673
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Comment: Comment: How to use Nextflow to call scripts from different environments?
5 months ago by O.rka ▴ 720
1
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2
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673
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How to use Nextflow to call scripts from different environments?
anaconda conda nextflow
5 months ago by O.rka ▴ 720
2
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1
reply
485
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 ▴ 720
2
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3
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730
views
How to check if my sequence is DNA or Protein in BioPython?
genomics biopython fasta
updated 6 months ago by 21k • written 6 months ago by ▴ 720
1
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1
reply
624
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 ▴ 720
1
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0
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624
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Answer: Answer: How to download taxonomy/lineage/taxonid information for JGI genome organism co
6 months ago by O.rka ▴ 720
0
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0
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565
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Comment: Comment: Why are some HUMAnN features in [name]_pathabundance.tsv missing taxonomy?
7 months ago by O.rka ▴ 720
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2
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565
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Why are some HUMAnN features in [name]_pathabundance.tsv missing taxonomy?
metagenomics metabolism humann biobakery metatranscriptomics
7 months ago by O.rka ▴ 720
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1
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466
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 ▴ 720
1
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3
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687
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 ▴ 720
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0
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687
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Comment: Comment: How to convert between UniRef50 to EC/enzyme number?
7 months ago by O.rka ▴ 720
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0
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704
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Comment: Comment: How to run TRUST4 for BCR/TCR detection using 10X data?
8 months ago by O.rka ▴ 720
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2
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704
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How to run TRUST4 for BCR/TCR detection using 10X data?
immunology trust4 illumina 10x
8 months ago by O.rka ▴ 720
7
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9
replies
1.9k
views
6 follow
How can I transfer gene models to a new assembly?
gene Assembly
updated 9 months ago by 8.4k • written 4.1 years ago by ▴ 720
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1
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813
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Comment: Comment: When counting ASVs in DADA2, does a hit/count only occur at 100% alignment perce
9 months ago by O.rka ▴ 720
0
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1
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1.9k
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Answer: Answer: How can I transfer gene models to a new assembly?
9 months ago by O.rka ▴ 720
3
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3
replies
813
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When counting ASVs in DADA2, does a hit/count only occur at 100% alignment percent identity?
metagenomics qiime2 amplicon 16s dada2
updated 9 months ago by 3.6k • written 9 months ago by ▴ 720
0
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0
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357
views
What criteria are used to determine significant HMMER hits?
kegg protein kofamscan annotation metagenomics
9 months ago by O.rka ▴ 720
0
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1
reply
609
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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 ▴ 720
3
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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 11 months ago by 15k • written 2.8 years ago by ▴ 720
0
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1
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1.7k
views
Comment: Comment: How can I speed up wget from UniProt for UniRef90/50 fasta?
12 months ago by O.rka ▴ 720
0
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1
reply
1.7k
views
Comment: Comment: How can I speed up wget from UniProt for UniRef90/50 fasta?
12 months ago by O.rka ▴ 720
0
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1
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1.7k
views
Comment: Comment: How can I speed up wget from UniProt for UniRef90/50 fasta?
12 months ago by O.rka ▴ 720
0
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7
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1.7k
views
How can I speed up wget from UniProt for UniRef90/50 fasta?
wget download uniprot uniref
updated 12 months ago by ★ 27k • written 12 months ago by ▴ 720
0
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0
replies
24k
views
Comment: Comment: Variant call format (VCF) file, how to get statistics per sample?
12 months ago by O.rka ▴ 720
0
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0
replies
1.2k
views
Comment: Comment: Should you specify "-p" for paired end reads using featureCounts?
12 months ago by O.rka ▴ 720
0
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1
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1.2k
views
Comment: Comment: Should you specify "-p" for paired end reads using featureCounts?
12 months ago by O.rka ▴ 720
4
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6
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1.2k
views
Should you specify "-p" for paired end reads using featureCounts?
fastq rnaseq genomics
12 months ago by O.rka ▴ 720
0
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0
replies
293
views
How can I get taxa relative abundances from HUMAnN?
metagenomics humann biobakery metatranscriptomics
13 months ago by O.rka ▴ 720
0
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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 ▴ 720
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1
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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 ▴ 720
5
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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 ▴ 720
0
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1
reply
907
views
Comment: Comment: How can I determine the number of detected genes and detected transcripts/isofor
13 months ago by O.rka ▴ 720
0
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1
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907
views
Comment: Comment: How can I determine the number of detected genes and detected transcripts/isofor
13 months ago by O.rka ▴ 720
0
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5
replies
907
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 ▴ 720
0
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0
replies
356
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Why did I get more unique genes than unique transcripts w/ STAR -> featureCounts?
rnaseq genomics star fastq alignment
14 months ago by O.rka ▴ 720
0
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1
reply
1.2k
views
Comment: Comment: How do you download from CyVerse using FTP or wget?
14 months ago by O.rka ▴ 720
0
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2
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1.2k
views
Comment: Comment: How do you download from CyVerse using FTP or wget?
14 months ago by O.rka ▴ 720
8
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6
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1.2k
views
How do you download from CyVerse using FTP or wget?
cyverse
updated 13 months ago by 43k • written 14 months ago by ▴ 720
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 ▴ 720
0
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0
replies
742
views
Comment: Comment: t2t human reference genome for RNA-seq
14 months ago by O.rka ▴ 720
408 results • Page 1 of 9
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