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2
votes
2
replies
337
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein FASTA alignment
updated 24 days ago by 43k • written 25 days ago by ▴ 140
2
votes
2
replies
395
views
Would you recommend me any tool to assign protein family membership to an aminoacidic fasta file?
protein-annotation fasta
updated 8 weeks ago by ★ 2.5k • written 3 months ago by ▴ 140
5
votes
3
replies
752
views
What are unbinned contigs ?
binning MAGs metagenomics
updated 7 months ago by ★ 27k • written 7 months ago by ▴ 140
0
votes
1
reply
411
views
Any idea to plot ANI calculation results ?
genomes ANI FastANI
updated 7 months ago by ★ 27k • written 7 months ago by ▴ 140
0
votes
0
replies
209
views
Help on dendrimer building
dendrimer gromacs molecular-dynamics
7 months ago by v.berriosfarias ▴ 140
0
votes
1
reply
480
views
Any tutorial to graph a metabolic pathway from a metabolic model ?
R GEM python gapseq
updated 9 months ago by ▴ 50 • written 9 months ago by ▴ 140
2
votes
3
replies
983
views
Would you recommend me a binning tool ?
MAGs metagenomics binning
updated 10 months ago by ★ 27k • written 10 months ago by ▴ 140
0
votes
1
reply
717
views
How to add a refseq() slot to a MAG based phyloseq object ?
phyloseq fasta R MAG
updated 10 months ago by 3.6k • written 10 months ago by ▴ 140
4
votes
3
replies
1.6k
views
Trying to use hmmer to search genes over metagenome assembled genomes
MAGs genes hmmer
11 months ago by v.berriosfarias ▴ 140
2
votes
2
replies
894
views
featureCounts: ERROR: failed to find the gene identifier attribute
gtf featureCounts subread
updated 11 months ago by 142k • written 11 months ago by ▴ 140
0
votes
0
replies
327
views
Error when converting hmmsearch output to gff file
hmmer2gff gff hmmer
12 months ago by v.berriosfarias ▴ 140
1
vote
1
reply
484
views
error when converting hmmer table to off table
hmmer2gff gff hmmer
updated 12 months ago by 142k • written 12 months ago by ▴ 140
4
votes
3
replies
1.6k
views
How to retrieve fastq files from NCBI using SRA accessions?
SRA fastq-dump
updated 13 months ago by 43k • written 2.1 years ago by ▴ 140
2
votes
3
replies
816
views
Any way to retrieve the annotation information of genomes under a bioproject ? (NCBI)
NCBI PGAP Bioproject annotation
13 months ago by v.berriosfarias ▴ 140
1
vote
1
reply
493
views
Assembly at lineage level from shotgun data ?
fungus MAGs assembly lineage
13 months ago by v.berriosfarias ▴ 140
1
vote
4
replies
640
views
trying to look the version of the programs under miniconda3 directory
miniconda3 versions
updated 15 months ago by 82k • written 15 months ago by ▴ 140
1
vote
0
replies
516
views
Calculating read abundances across MAGs (question)
abundance Metagenomics paired-reads
16 months ago by v.berriosfarias ▴ 140
0
votes
2
replies
5.9k
views
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option
metawrap concoct conda openblas
updated 16 months ago by ▴ 60 • written 3.1 years ago by ▴ 140
0
votes
0
replies
350
views
Problem with Autometa binning tool
autometa
18 months ago by v.berriosfarias ▴ 140
2
votes
2
replies
1.2k
views
megahit error exit code 6
megahit
updated 19 months ago by ★ 27k • written 19 months ago by ▴ 140
8
votes
6
replies
4.1k
views
How to cat 2 paired end reads files together in one file using loops for multiple libraries ?
paired-end-reads cat loops bash
updated 19 months ago by ▴ 20 • written 3.0 years ago by ▴ 140
4
votes
6
replies
1.4k
views
Does ASVs IDs from dada2 have specific taxonomic assignments?
dada2 R ASVs
updated 7 months ago by 3.6k • written 20 months ago by ▴ 140
0
votes
0
replies
370
views
any way to merge functions of kegg orthologs database?
functional-profile metagenomics data-wrangling
21 months ago by v.berriosfarias ▴ 140
2
votes
1
reply
1.5k
views
How to import conda environments to Rstudio?
Estudio conda
updated 22 months ago by 3.9k • written 22 months ago by ▴ 140
0
votes
0
replies
338
views
Is it normal that my amplicon sequence variants (ASVs) have gaps ?
ASVs DADA2 fasta
22 months ago by v.berriosfarias ▴ 140
0
votes
3
replies
750
views
How to add taxonomic information to fasta headers
MAGs taxonomy fasta
updated 22 months ago by 21k • written 22 months ago by ▴ 140
3
votes
5
replies
882
views
How to remove [ACTG] from file names in bash
bash substring
updated 22 months ago by 21k • written 22 months ago by ▴ 140
2
votes
3
replies
734
views
any tool for searching duplicated or redundant sequences in a database?
fasta database
updated 23 months ago by ▴ 380 • written 2.0 years ago by ▴ 140
0
votes
0
replies
316
views
problem with gene abundance calculation
bam gtf bash R GFF
23 months ago by v.berriosfarias ▴ 140
3
votes
2
replies
655
views
Problem when converting from blast output table to GTF file.
gene GTF GFF
updated 23 months ago by 8.6k • written 23 months ago by ▴ 140
0
votes
1
reply
885
views
How to normalize gene abundance from metagenomic data?
gene-abundance normalization R metagenomics
updated 23 months ago by 10k • written 23 months ago by ▴ 140
3
votes
4
replies
767
views
Struggling with some data visualization in R
ggplot2 visualization R
updated 23 months ago by 11k • written 23 months ago by ▴ 140
1
vote
2
replies
910
views
gene abundance profiling from metagenomes
gene-abundance mapping metagenomics
23 months ago by v.berriosfarias ▴ 140
0
votes
1
reply
640
views
GRanges strand identification
GRanges R bam
updated 23 months ago by 3.9k • written 23 months ago by ▴ 140
1
vote
1
reply
628
views
statistical question (different number of gene orthologs on database)
database statistics
updated 24 months ago by 10k • written 24 months ago by ▴ 140
2
votes
4
replies
908
views
How to rearrange fasta headers
fasta R bash string
updated 2.0 years ago by 21k • written 2.0 years ago by ▴ 140
0
votes
0
replies
575
views
MMseqs2 with paired end reads?
protein-profiling mmseqs2
2.0 years ago by v.berriosfarias ▴ 140
3
votes
5
replies
1.0k
views
retrieving paired end sequencing data with fasts-dump
NCBI fastq sra-toolkit
updated 2.0 years ago by 100k • written 2.0 years ago by ▴ 140
0
votes
0
replies
344
views
How to perform a biplot having a genomic distance matrix and environmental metadata
PCoA ampvis2 R biplot vegan
2.1 years ago by v.berriosfarias ▴ 140
3
votes
3
replies
1.1k
views
retrieveing gene list from NCBI
NCBI gene perl
updated 2.4 years ago by 142k • written 2.4 years ago by ▴ 140
2
votes
3
replies
3.5k
views
Could NOT find ZLIB while running cmake
zlib cmake conda racon
updated 2.4 years ago by ★ 4.7k • written 2.4 years ago by ▴ 140
0
votes
0
replies
499
views
Pacbio and illumina assembly question
Pacbio assembly racon illumina
2.4 years ago by v.berriosfarias ▴ 140
2
votes
4
replies
1.5k
views
How to add taxonomic information for each fasta header ?
awk taxonomy FASTA
updated 2.4 years ago by 8.5k • written 2.4 years ago by ▴ 140
1
vote
2
replies
1.4k
views
how to create a custom database (GTDB) ?
MAGs GTDB databases
2.2 years ago by v.berriosfarias ▴ 140
1
vote
1
reply
705
views
How to retrieve all the nucleotide sequences in fasta format of all 'nucleotide' hyperlinks from a specie accesion from NCBI?
ncbi fasta
updated 2.5 years ago by 142k • written 2.5 years ago by ▴ 140
1
vote
3
replies
2.0k
views
which sequence adapter trimming tool should i use for my illumina 101pb reads ?
cutadapt alignment seed illumina
updated 2.6 years ago by ▴ 60 • written 3.5 years ago by ▴ 140
1
vote
2
replies
1.7k
views
parsing gbk files (antismash result)
awk biopython gbk antismash bash
2.7 years ago by v.berriosfarias ▴ 140
5
votes
5
replies
1.7k
views
how to remove a substring for multiple file names?
string bash
15 months ago by v.berriosfarias ▴ 140
1
vote
2
replies
643
views
is there a proper way to choose clusters in hierarchical clustering?
Hierarchical-clustering dendogram R
updated 2.9 years ago by 3.2k • written 2.9 years ago by ▴ 140
5
votes
4
replies
2.6k
views
distance matrix as input in R clustering functions ?
k-medioids-genetic-distances-mash R Clustering
updated 2.9 years ago by 27k • written 2.9 years ago by ▴ 140
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