Profile Posts Awards
Show
all questions tools blogs news tutorials forum answers comments
Showing : questions
2
votes
2
replies
367
views
Would you recommend me any tool to assign protein family membership to an aminoacidic fasta file?
protein-annotation fasta
updated 4 weeks ago by ★ 2.5k • written 11 weeks ago by ▴ 140
5
votes
3
replies
682
views
What are unbinned contigs ?
binning MAGs metagenomics
updated 6 months ago by ★ 27k • written 6 months ago by ▴ 140
0
votes
1
reply
382
views
Any idea to plot ANI calculation results ?
genomes ANI FastANI
updated 6 months ago by ★ 27k • written 6 months ago by ▴ 140
0
votes
0
replies
194
views
Help on dendrimer building
dendrimer gromacs molecular-dynamics
6 months ago by v.berriosfarias ▴ 140
0
votes
1
reply
448
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
897
views
Would you recommend me a binning tool ?
MAGs metagenomics binning
updated 9 months ago by ★ 27k • written 9 months ago by ▴ 140
0
votes
1
reply
671
views
How to add a refseq() slot to a MAG based phyloseq object ?
phyloseq fasta R MAG
updated 9 months ago by 3.6k • written 9 months ago by ▴ 140
4
votes
3
replies
1.5k
views
Trying to use hmmer to search genes over metagenome assembled genomes
MAGs genes hmmer
10 months ago by v.berriosfarias ▴ 140
2
votes
2
replies
860
views
featureCounts: ERROR: failed to find the gene identifier attribute
gtf featureCounts subread
updated 10 months ago by 141k • written 10 months ago by ▴ 140
0
votes
0
replies
315
views
Error when converting hmmsearch output to gff file
hmmer2gff gff hmmer
11 months ago by v.berriosfarias ▴ 140
1
vote
1
reply
458
views
error when converting hmmer table to off table
hmmer2gff gff hmmer
updated 11 months ago by 141k • written 11 months ago by ▴ 140
4
votes
3
replies
1.5k
views
How to retrieve fastq files from NCBI using SRA accessions?
SRA fastq-dump
updated 12 months ago by 43k • written 2.0 years ago by ▴ 140
2
votes
3
replies
797
views
Any way to retrieve the annotation information of genomes under a bioproject ? (NCBI)
NCBI PGAP Bioproject annotation
12 months ago by v.berriosfarias ▴ 140
1
vote
1
reply
481
views
Assembly at lineage level from shotgun data ?
fungus MAGs assembly lineage
12 months ago by v.berriosfarias ▴ 140
1
vote
4
replies
613
views
trying to look the version of the programs under miniconda3 directory
miniconda3 versions
updated 14 months ago by 81k • written 14 months ago by ▴ 140
1
vote
0
replies
491
views
Calculating read abundances across MAGs (question)
abundance Metagenomics paired-reads
15 months ago by v.berriosfarias ▴ 140
0
votes
2
replies
5.8k
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 15 months ago by ▴ 60 • written 3.0 years ago by ▴ 140
0
votes
0
replies
333
views
Problem with Autometa binning tool
autometa
17 months ago by v.berriosfarias ▴ 140
2
votes
2
replies
1.1k
views
megahit error exit code 6
megahit
updated 18 months ago by ★ 27k • written 18 months ago by ▴ 140
8
votes
6
replies
4.0k
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 18 months ago by ▴ 10 • written 2.9 years ago by ▴ 140
4
votes
6
replies
1.3k
views
Does ASVs IDs from dada2 have specific taxonomic assignments?
dada2 R ASVs
updated 6 months ago by 3.6k • written 19 months ago by ▴ 140
0
votes
0
replies
359
views
any way to merge functions of kegg orthologs database?
functional-profile metagenomics data-wrangling
20 months ago by v.berriosfarias ▴ 140
2
votes
1
reply
1.4k
views
How to import conda environments to Rstudio?
Estudio conda
updated 21 months ago by 3.9k • written 21 months ago by ▴ 140
0
votes
0
replies
324
views
Is it normal that my amplicon sequence variants (ASVs) have gaps ?
ASVs DADA2 fasta
21 months ago by v.berriosfarias ▴ 140
0
votes
3
replies
718
views
How to add taxonomic information to fasta headers
MAGs taxonomy fasta
updated 21 months ago by 21k • written 21 months ago by ▴ 140
3
votes
5
replies
837
views
How to remove [ACTG] from file names in bash
bash substring
updated 21 months ago by 21k • written 21 months ago by ▴ 140
2
votes
3
replies
704
views
any tool for searching duplicated or redundant sequences in a database?
fasta database
updated 22 months ago by ▴ 380 • written 23 months ago by ▴ 140
0
votes
0
replies
307
views
problem with gene abundance calculation
bam gtf bash R GFF
22 months ago by v.berriosfarias ▴ 140
3
votes
2
replies
622
views
Problem when converting from blast output table to GTF file.
gene GTF GFF
updated 22 months ago by 8.5k • written 22 months ago by ▴ 140
0
votes
1
reply
859
views
How to normalize gene abundance from metagenomic data?
gene-abundance normalization R metagenomics
updated 22 months ago by 10k • written 22 months ago by ▴ 140
3
votes
4
replies
742
views
Struggling with some data visualization in R
ggplot2 visualization R
updated 22 months ago by 11k • written 22 months ago by ▴ 140
1
vote
2
replies
877
views
gene abundance profiling from metagenomes
gene-abundance mapping metagenomics
22 months ago by v.berriosfarias ▴ 140
0
votes
1
reply
610
views
GRanges strand identification
GRanges R bam
updated 22 months ago by 3.9k • written 22 months ago by ▴ 140
1
vote
1
reply
615
views
statistical question (different number of gene orthologs on database)
database statistics
updated 23 months ago by 10k • written 23 months ago by ▴ 140
2
votes
4
replies
878
views
How to rearrange fasta headers
fasta R bash string
updated 23 months ago by 21k • written 23 months ago by ▴ 140
0
votes
0
replies
560
views
MMseqs2 with paired end reads?
protein-profiling mmseqs2
23 months ago by v.berriosfarias ▴ 140
3
votes
5
replies
984
views
retrieving paired end sequencing data with fasts-dump
NCBI fastq sra-toolkit
updated 23 months ago by 100k • written 23 months ago by ▴ 140
0
votes
0
replies
336
views
How to perform a biplot having a genomic distance matrix and environmental metadata
PCoA ampvis2 R biplot vegan
2.0 years ago by v.berriosfarias ▴ 140
3
votes
3
replies
1.0k
views
retrieveing gene list from NCBI
NCBI gene perl
updated 2.3 years ago by 141k • written 2.3 years ago by ▴ 140
2
votes
3
replies
3.4k
views
Could NOT find ZLIB while running cmake
zlib cmake conda racon
updated 2.3 years ago by ★ 4.7k • written 2.3 years ago by ▴ 140
0
votes
0
replies
488
views
Pacbio and illumina assembly question
Pacbio assembly racon illumina
2.3 years ago by v.berriosfarias ▴ 140
2
votes
4
replies
1.4k
views
How to add taxonomic information for each fasta header ?
awk taxonomy FASTA
updated 2.3 years ago by 8.4k • written 2.3 years ago by ▴ 140
1
vote
2
replies
1.4k
views
how to create a custom database (GTDB) ?
MAGs GTDB databases
2.1 years ago by v.berriosfarias ▴ 140
1
vote
1
reply
693
views
How to retrieve all the nucleotide sequences in fasta format of all 'nucleotide' hyperlinks from a specie accesion from NCBI?
ncbi fasta
updated 2.4 years ago by 141k • written 2.4 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 2.5 years ago by ▴ 60 • written 3.4 years ago by ▴ 140
1
vote
2
replies
1.7k
views
parsing gbk files (antismash result)
awk biopython gbk antismash bash
2.6 years ago by v.berriosfarias ▴ 140
5
votes
5
replies
1.6k
views
how to remove a substring for multiple file names?
string bash
14 months ago by v.berriosfarias ▴ 140
1
vote
2
replies
622
views
is there a proper way to choose clusters in hierarchical clustering?
Hierarchical-clustering dendogram R
updated 2.8 years ago by 3.2k • written 2.8 years ago by ▴ 140
5
votes
4
replies
2.5k
views
distance matrix as input in R clustering functions ?
k-medioids-genetic-distances-mash R Clustering
updated 2.8 years ago by 27k • written 2.8 years ago by ▴ 140
0
votes
2
replies
753
views
Viral taxonomic classification question
taxonomic-classification viral-metagenomics
2.8 years ago by v.berriosfarias ▴ 140
68 results • Page 1 of 2
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6