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162
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Help interpreting KEGG module definitions for converting to NetworkX graph
definition kegg module database genomics
11 days ago by O.rka ▴ 720
0
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0
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170
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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
27 days ago by O.rka ▴ 720
1
vote
3
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469
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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 29 days ago by ★ 27k • written 4 weeks ago by ▴ 720
0
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2
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366
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Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics metacyc enzyme biobakery humann
6 weeks ago by O.rka ▴ 720
0
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2
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374
views
Why are gene models from JGI non-sense when using AGAT to to extract proteins?
translation models gif gene cgi
8 weeks ago by O.rka ▴ 720
1
vote
1
reply
538
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 3 months ago by ▴ 10 • written 5 months ago by ▴ 720
0
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1
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594
views
How can I calculate the percent of bases covered in the query assembly relative to the reference assembly?
samtools
updated 4 months ago by ★ 2.0k • written 4 months ago by ▴ 720
1
vote
2
replies
712
views
How to use Nextflow to call scripts from different environments?
anaconda conda nextflow
5 months ago by O.rka ▴ 720
2
votes
1
reply
527
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam sam reads fastq
updated 6 months ago by 13k • written 6 months ago by ▴ 720
2
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3
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767
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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
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648
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How to download taxonomy/lineage/taxonid information for JGI genome organism codes? (e.g., MycoCosm and PhycoCosm)
jgi genomics phycocosm mycocosm taxonomy
7 months ago by O.rka ▴ 720
0
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2
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582
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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
0
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1
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480
views
How to download genomes and proteins from JGI in bulk via the command line?
jgi cli
updated 8 months ago by 44k • written 8 months ago by ▴ 720
1
vote
3
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704
views
How to convert between UniRef50 to EC/enzyme number?
Uniref conversion uniprot enzyme
updated 8 months ago by ★ 2.4k • written 8 months ago by ▴ 720
0
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2
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741
views
How to run TRUST4 for BCR/TCR detection using 10X data?
immunology trust4 illumina 10x
8 months ago by O.rka ▴ 720
7
votes
9
replies
1.9k
views
6 follow
How can I transfer gene models to a new assembly?
gene Assembly
updated 9 months ago by 8.5k • written 4.2 years ago by ▴ 720
3
votes
3
replies
841
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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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362
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What criteria are used to determine significant HMMER hits?
kegg protein kofamscan annotation metagenomics
10 months ago by O.rka ▴ 720
0
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1
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619
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Using tRNAscan-SE for mitochondria tRNA from microeukaryotes like protists and yeast?
trnascan yeasts eukaryotes protists trna
updated 11 months ago by ★ 1.2k • written 11 months ago by ▴ 720
3
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2
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2.2k
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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7
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1.8k
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
4
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6
replies
1.2k
views
Should you specify "-p" for paired end reads using featureCounts?
fastq rnaseq genomics
13 months ago by O.rka ▴ 720
0
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0
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299
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How can I get taxa relative abundances from HUMAnN?
metagenomics humann biobakery metatranscriptomics
13 months ago by O.rka ▴ 720
5
votes
9
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2.2k
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 14 months ago by ▴ 720
0
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5
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925
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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 14 months ago by 142k • written 14 months ago by ▴ 720
0
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0
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360
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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
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 14 months ago by 44k • 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 44k • written 3.0 years ago by ▴ 720
1
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4
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2.0k
views
How could I "recreate" UniRef50/UniRef90 with MMSEQS2?
clustering proteins annotation mmseqs2
updated 10 months ago by • 0 • written 14 months ago by ▴ 720
1
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2
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1.9k
views
Are there any tools that can create a very basic GTF file from contig sequences (no annotations really needed) ?
Assembly mapping
14 months ago by O.rka ▴ 720
0
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0
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381
views
What's the state-of-the-art for gene calling in eukaryotic transcriptomics?
modeling eukaryotic transcriptomics call gene
16 months ago by O.rka ▴ 720
3
votes
5
replies
1.1k
views
How can I run multiple sequence alignment for a large number of proteins (~10k)
muscle msa protein multiple alignment sequence
updated 16 months ago by ★ 27k • written 16 months ago by ▴ 720
1
vote
2
replies
651
views
What's best practice when determining a degenerate base when creating a primer?
primer-design alignment genomics
16 months ago by O.rka ▴ 720
1
vote
6
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1.4k
views
Any command line tools that can design primers from a multiple sequence alignment?
primer-design genomics cli
16 months ago by O.rka ▴ 720
9
votes
6
replies
1.6k
views
What in silico PCR commandline tool do you use that can handle IUPAC characters?
pcr amplicon primer
updated 7 weeks ago by 44k • written 17 months ago by ▴ 720
3
votes
3
replies
788
views
How to find full length ribosomal sequences for fungi?
ncbi ribosomal fungi nt
17 months ago by O.rka ▴ 720
0
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0
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328
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How to estimate the memory requirements for Diamond given the database and query protein sizes?
alignment diamond memory requirements
17 months ago by O.rka ▴ 720
0
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4
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715
views
How to "enrich" a large set of proteins (>11M) for protein hits in UniRef90?
uniref proteins alignment
17 months ago by O.rka ▴ 720
3
votes
4
replies
1.4k
views
How to extract unmapped reads if you have paired end reads (fastq) and mapped BAM file?
fastq bam sam reads
19 months ago by O.rka ▴ 720
2
votes
2
replies
906
views
What's the benefit of using the `no_alt_analysis_set` Bowtie2 index over the primary assembly?
human rnaseq mapping metagenomics
updated 19 months ago by 82k • written 19 months ago by ▴ 720
0
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1
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683
views
Is there a tool that quantifies “spatial coverage”, that is what percentage of a reference assembly has a read mapped to it?
coverage genomics mapping assembly
updated 21 months ago by 142k • written 21 months ago by ▴ 720
0
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2
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563
views
How to calculate position-specific fastq stats?
rnaseq fastq metagenomics genomics
21 months ago by O.rka ▴ 720
0
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3
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1.7k
views
Are there any tools that automatically detect where to truncate forward and reverse reads for 16S (DADA2)?
16s dada2 illumina metagenomics qiime2
21 months ago by O.rka ▴ 720
1
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3
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1.2k
views
Is it required for all sequences to be same length when clustering OTUs in metagenomics (ONT Nanopore)
otu metagenomics clustering nanopore
updated 22 months ago by 3.2k • written 22 months ago by ▴ 720
0
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2
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655
views
What percent identity is recommended for detecting protein homology within a species?
alignment genomics proteomics
22 months ago by O.rka ▴ 720
1
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6
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1.7k
views
Is there a tool that calculates genome coverage? (e.g., 1X, 10X, 100X)
ncbi metagenomics submission
22 months ago by O.rka ▴ 720
0
votes
1
reply
486
views
Software to produce position-specific conservation of multiple sequence alignment results?
transcriptomics genomics alignment proteomics
updated 23 months ago by ★ 27k • written 23 months ago by ▴ 720
0
votes
1
reply
1.1k
views
How to count the number of multimapped reads from a bam file?
rnaseq mapping bowtie2 featurecounts
updated 23 months ago by ★ 1.4k • written 23 months ago by ▴ 720
1
vote
1
reply
938
views
Advice on mapping reads to polyploid de-novo assembly
assembly RNA-Seq
updated 23 months ago by 6.4k • written 4.3 years ago by ▴ 720
0
votes
1
reply
592
views
How do you predict regions on a protein that are exposed on the cell surface?
protein antibody hmm domain
updated 23 months ago by ★ 27k • written 23 months ago by ▴ 720
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