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0
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187
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Comment: Comment: How to remove [ACTG] from file names in bash
2 days ago by v.berriosfarias ▴ 50
2
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5
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187
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How to remove [ACTG] from file names in bash
bash substring
updated 1 day ago by 21k • written 2 days ago by ▴ 50
2
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3
replies
231
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any tool for searching duplicated or redundant sequences in a database?
fasta database
updated 10 days ago by ▴ 360 • written 8 weeks ago by ▴ 50
0
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0
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81
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problem with gene abundance calculation
bam gtf bash R GFF
15 days ago by v.berriosfarias ▴ 50
0
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0
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139
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Comment: Comment: Problem when converting from blast output table to GTF file.
17 days ago by v.berriosfarias ▴ 50
3
votes
2
replies
139
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Problem when converting from blast output table to GTF file.
gene GTF GFF
updated 16 days ago by ★ 7.1k • written 17 days ago by ▴ 50
0
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1
reply
155
views
How to normalize gene abundance from metagenomic data?
gene-abundance normalization R metagenomics
updated 18 days ago by 8.9k • written 18 days ago by ▴ 50
3
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4
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319
views
Struggling with some data visualization in R
ggplot2 visualization R
updated 24 days ago by 9.5k • written 24 days ago by ▴ 50
0
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0
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231
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Comment: Comment: gene abundance profiling from metagenomes
26 days ago by v.berriosfarias ▴ 50
1
vote
2
replies
231
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gene abundance profiling from metagenomes
gene-abundance mapping metagenomics
26 days ago by v.berriosfarias ▴ 50
0
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1
reply
190
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GRanges strand identification
GRanges R bam
updated 29 days ago by ★ 2.9k • written 29 days ago by ▴ 50
1
vote
1
reply
212
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statistical question (different number of gene orthologs on database)
database statistics
updated 5 weeks ago by 8.9k • written 6 weeks ago by ▴ 50
0
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1
reply
269
views
Comment: Comment: How to rearrange fasta headers
6 weeks ago by v.berriosfarias ▴ 50
2
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4
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269
views
How to rearrange fasta headers
fasta R bash string
updated 6 weeks ago by 21k • written 6 weeks ago by ▴ 50
0
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0
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98
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MMseqs2 with paired end reads?
protein-profiling mmseqs2
7 weeks ago by v.berriosfarias ▴ 50
0
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0
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395
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Comment: Comment: retrieving paired end sequencing data with fasts-dump
8 weeks ago by v.berriosfarias ▴ 50
0
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0
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395
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Comment: Comment: retrieving paired end sequencing data with fasts-dump
8 weeks ago by v.berriosfarias ▴ 50
3
votes
5
replies
395
views
retrieving paired end sequencing data with fasts-dump
NCBI fastq sra-toolkit
updated 8 weeks ago by 93k • written 8 weeks ago by ▴ 50
0
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0
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91
views
How to perform a biplot having a genomic distance matrix and environmental metadata
PCoA ampvis2 R biplot vegan
10 weeks ago by v.berriosfarias ▴ 50
1
vote
1
reply
171
views
How to retrieve fastq files from NCBI using SRA accessions?
SRA fastq-dump
updated 10 weeks ago by 117k • written 10 weeks ago by ▴ 50
0
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0
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420
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Comment: Comment: how to create a custom database (GTDB) ?
3 months ago by v.berriosfarias ▴ 50
3
votes
3
replies
423
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retrieveing gene list from NCBI
NCBI gene perl
updated 6 months ago by 117k • written 6 months ago by ▴ 50
2
votes
3
replies
1.2k
views
Could NOT find ZLIB while running cmake
zlib cmake conda racon
updated 6 months ago by ★ 4.4k • written 6 months ago by ▴ 50
0
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0
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189
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Pacbio and illumina assembly question
Pacbio assembly racon illumina
6 months ago by v.berriosfarias ▴ 50
0
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1
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546
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Comment: Comment: How to add taxonomic information for each fasta header ?
updated 6 months ago by 7.3k • written 6 months ago by ▴ 50
2
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4
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546
views
How to add taxonomic information for each fasta header ?
awk taxonomy FASTA
updated 6 months ago by 7.3k • written 6 months ago by ▴ 50
0
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0
replies
1.6k
views
Comment: Comment: Difference between a bin and a MAG
6 months ago by v.berriosfarias ▴ 50
0
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1
reply
1.6k
views
Comment: Comment: Difference between a bin and a MAG
6 months ago by v.berriosfarias ▴ 50
1
vote
2
replies
420
views
how to create a custom database (GTDB) ?
MAGs GTDB databases
3 months ago by v.berriosfarias ▴ 50
1
vote
1
reply
390
views
How to retrieve all the nucleotide sequences in fasta format of all 'nucleotide' hyperlinks from a specie accesion from NCBI?
ncbi fasta
updated 7 months ago by 117k • written 7 months ago by ▴ 50
1
vote
3
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1.2k
views
which sequence adapter trimming tool should i use for my illumina 101pb reads ?
cutadapt alignment seed illumina
updated 8 months ago by ▴ 30 • written 19 months ago by ▴ 50
0
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0
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620
views
Comment: Comment: parsing gbk files (antismash result)
10 months ago by v.berriosfarias ▴ 50
1
vote
2
replies
620
views
parsing gbk files (antismash result)
awk biopython gbk antismash bash
10 months ago by v.berriosfarias ▴ 50
3
votes
4
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518
views
how to remove a substring for multiple file names?
string bash
updated 11 months ago by 21k • written 11 months ago by ▴ 50
0
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0
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518
views
Comment: Comment: how to remove a substring for multiple file names?
11 months ago by v.berriosfarias ▴ 50
0
votes
1
reply
1.0k
views
Comment: Comment: distance matrix as input in R clustering functions ?
12 months ago by v.berriosfarias ▴ 50
1
vote
2
replies
334
views
is there a proper way to choose clusters in hierarchical clustering?
Hierarchical-clustering dendogram R
updated 12 months ago by ★ 2.5k • written 12 months ago by ▴ 50
4
votes
4
replies
1.0k
views
distance matrix as input in R clustering functions ?
k-medioids-genetic-distances-mash R Clustering
updated 12 months ago by 25k • written 12 months ago by ▴ 50
0
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0
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351
views
Comment: Comment: Viral taxonomic classification question
12 months ago by v.berriosfarias ▴ 50
0
votes
2
replies
351
views
Viral taxonomic classification question
taxonomic-classification viral-metagenomics
12 months ago by v.berriosfarias ▴ 50
4
votes
1
reply
315
views
Does anyone know if there is an implementation of overlaping kmeans algorithm in R ?
r partitional-clustering kmeans
updated 12 months ago by ★ 20k • written 12 months ago by ▴ 50
0
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1
reply
311
views
how to import multiple fastq files from NCBI without using fastq-dump?
curl wget multi-samples importing
updated 13 months ago by 117k • written 13 months ago by ▴ 50
0
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1
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1.2k
views
Comment: Comment: How to cat 2 paired end reads files together in one file using loops for multip
13 months ago by v.berriosfarias ▴ 50
0
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1
reply
1.2k
views
Comment: Comment: How to cat 2 paired end reads files together in one file using loops for multip
13 months ago by v.berriosfarias ▴ 50
4
votes
5
replies
1.2k
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 13 months ago by 62k • written 13 months ago by ▴ 50
0
votes
1
reply
2.5k
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 14 months ago by ★ 20k • written 14 months ago by ▴ 50
0
votes
1
reply
653
views
Maxbin2 usage for paired end reads
binning paired-end-reads
updated 12 months ago by • 0 • written 14 months ago by ▴ 50
0
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0
replies
248
views
should I scale a MASH matrix ?
scale MASH
14 months ago by v.berriosfarias ▴ 50
0
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0
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647
views
Comment: Comment: making a PCA from MASH distance result
14 months ago by v.berriosfarias ▴ 50
0
votes
1
reply
4.7k
views
Comment: Comment: Installing perl modules on a conda environment produce changes out of the enviro
14 months ago by v.berriosfarias ▴ 50
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