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5
votes
5
replies
357
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 16 days ago by ▴ 40 • written 16 days ago by ▴ 150
0
votes
2
replies
349
views
BLAST using both nucleotides and taxonomic local databases
blast ncbi taxid taxonomy
updated 23 days ago by 142k • written 23 days ago by ▴ 150
4
votes
6
replies
546
views
Odd results with BLAST remote
blast remote NCBI
updated 4 weeks ago by ▴ 200 • written 4 weeks ago by ▴ 150
1
vote
3
replies
457
views
Extracting data from a local NCBI taxonomy database
R NCBI xml E-utilities Blast
updated 4 weeks ago by ▴ 60 • written 6 weeks ago by ▴ 150
1
vote
2
replies
261
views
Issue with making local BLAST database
R mitochodrial diatoms blast ncbi
updated 7 weeks ago by 43k • written 7 weeks ago by ▴ 150
4
votes
5
replies
504
views
Blastn frozen
blastn NCBI BLAST remote-blast
3 months ago by Begonia_pavonina ▴ 150
3
votes
7
replies
639
views
Blast NCBI online using R
R NCBI BLAST Rstudio
7 weeks ago by Begonia_pavonina ▴ 150
1
vote
3
replies
566
views
Formatting issues using DADA2 with the database EukRIbo
DADA2 Silva fasta metabarcoding EukRibo
3 months ago by Begonia_pavonina ▴ 150
7
votes
8
replies
1.3k
views
Problem with Mamba
snakemake mamba conda
updated 4 months ago by ▴ 80 • written 4 months ago by ▴ 150
0
votes
4
replies
604
views
Snakemake error AttributeError: 'Resources' object has no attribute 'tmpdir'
Python BWA Snakemake
updated 5 months ago by 13k • written 5 months ago by ▴ 150
3
votes
2
replies
820
views
Samtools index not working in Snakemake
snakemake samtools
updated 6 months ago by 13k • written 6 months ago by ▴ 150
5
votes
4
replies
611
views
Conda environment not named
snakemake conda
updated 6 months ago by 43k • written 6 months ago by ▴ 150
4
votes
9
replies
1.3k
views
Snakemake issue with wrappers
Python Snakemake
6 months ago by Begonia_pavonina ▴ 150
5
votes
9
replies
972
views
Wildcards in Snakemake
Python workflow Snakemake wrapper
updated 7 months ago by 22k • written 7 months ago by ▴ 150
1
vote
1
reply
472
views
Manage the wrappers in Snakemake
snakemake python
updated 7 months ago by 43k • written 7 months ago by ▴ 150
4
votes
5
replies
891
views
Snakemake alignment script
snakemake alignment
7 months ago by Begonia_pavonina ▴ 150
3
votes
6
replies
1.1k
views
The GATK "The given bam input has no sample names." error
GATK BWA
updated 9 months ago by 142k • written 9 months ago by ▴ 150
2
votes
1
reply
763
views
Calculate the kinship matrix from NGS data
PCangsd kinship BEAGLE ANGSD
updated 13 months ago by 10k • written 13 months ago by ▴ 150
0
votes
0
replies
768
views
How to get BEAGLE files from VCF with angsd?
angsd vcf populationgenetics beagle pcangsd
13 months ago by Begonia_pavonina ▴ 150
3
votes
3
replies
967
views
Using vcfR to group variants per annotations
vcf vcfR R
updated 14 months ago by ★ 2.0k • written 14 months ago by ▴ 150
1
vote
4
replies
1.3k
views
Filter out overlapping deletions from a VCF file.
vcf bcftools gvcf
15 months ago by Begonia_pavonina ▴ 150
0
votes
4
replies
1.5k
views
From VCF to BEAGLE format with multiple chromosomes
vcf vcftools beagle gvcf
12 months ago by Begonia_pavonina ▴ 150
0
votes
0
replies
404
views
Plot Phylogenetic tree with traits in Biopython
Biopython Phylo Python Phylogeny
18 months ago by Begonia_pavonina ▴ 150
1
vote
1
reply
1.1k
views
Labels colors in Bio.Phylo
Bio.Phylo Python BioPython
updated 19 months ago by 3.2k • written 19 months ago by ▴ 150
3
votes
2
replies
1.1k
views
Bootstraps values in iqtree
iqtree
19 months ago by Begonia_pavonina ▴ 150
5
votes
4
replies
1.8k
views
IQ-TREE stuck in selecting a substitution model with ModelFinder
substitution ModelFInder model IQ-TREE
updated 11 months ago by ▴ 870 • written 22 months ago by ▴ 150
7
votes
12
replies
4.3k
views
Snakemake 'Unexpected keyword ref in rule definition'
snakemake python
updated 2.3 years ago by 21k • written 2.3 years ago by ▴ 150
1
vote
2
replies
808
views
Multiple samples in PLINK
gvcf plink roh variants
2.3 years ago by Begonia_pavonina ▴ 150
1
vote
2
replies
1.3k
views
Confused about PED and MAP file
PED PLINK MAP detectRUNS
2.3 years ago by Begonia_pavonina ▴ 150
0
votes
0
replies
459
views
Label groups with samples names in snpgdsDrawTree (SNPRelate package)
SNPRelate
2.5 years ago by Begonia_pavonina ▴ 150
1
vote
2
replies
2.0k
views
No header in VCF file
VCF bcftools header
2.5 years ago by Begonia_pavonina ▴ 150
1
vote
2
replies
754
views
Plotting chromosomes and target capture baits
plotting target_capture Hyb-Seq R
2.7 years ago by Begonia_pavonina ▴ 150
0
votes
1
reply
2.1k
views
Missing read group in BAM files
BWA ValidateSamFile BAM GATK HybPiper
updated 2.8 years ago by 14k • written 2.8 years ago by ▴ 150
2
votes
1
reply
1.0k
views
Find and replace the RNAME field in BAM/SAM file
samtools bam loop sed sam
updated 3.0 years ago by 142k • written 3.0 years ago by ▴ 150
0
votes
0
replies
442
views
KeyError in the pipeline SECAPR
SECAPR Hyb-Seq locus_selection Python Key_error
3.0 years ago by Begonia_pavonina ▴ 150
0
votes
0
replies
526
views
SECAPR issue
SECAPR reads trimmomatic pipeline alignement
3.1 years ago by Begonia_pavonina ▴ 150
3
votes
8
replies
2.4k
views
blast2gff IndexError: list index out of range
blast2gff GFF BLAST Python blastn
updated 2.8 years ago by • 0 • written 3.7 years ago by ▴ 150
5
votes
7
replies
1.2k
views
Replace FASTA file headers
fasta FASTA sed loop
updated 3.6 years ago by 21k • written 3.6 years ago by ▴ 150
2
votes
2
replies
1.7k
views
Keep metadata gc column using GenomicRanges
ranges Iranges R
3.6 years ago by Begonia_pavonina ▴ 150
4
votes
4
replies
2.9k
views
merging overlaping ranges with GenomicRanges
R blast GenomicRanges range
updated 3.6 years ago by 22k • written 3.6 years ago by ▴ 150
3
votes
1
reply
2.1k
views
Length of scaffolds in a FASTA file
fasta genome bash scaffold
updated 3.7 years ago by 21k • written 3.7 years ago by ▴ 150
3
votes
7
replies
1.4k
views
edit FASTA file according to range positions
alignment fasta bed samtools
3.7 years ago by Begonia_pavonina ▴ 150
0
votes
1
reply
581
views
A piece of advice on subsetting genomes
gff fasta genome annotations blast
3.7 years ago by Begonia_pavonina ▴ 150
7
votes
2
replies
8.0k
views
GATK 3.8 and GATK 3.7 scripts
gatk alignment version repository
updated 3.8 years ago by ▴ 10 • written 4.0 years ago by ▴ 150
0
votes
0
replies
636
views
Clustering of SNPs toward same QUAL values
snp freebayes variants quality
updated 3.8 years ago by 20 • written 3.8 years ago by ▴ 150
1
vote
4
replies
1.9k
views
How to compare VCF files called from different reference genomes?
vcf Freebayes Picard SNP alignment
3.8 years ago by Begonia_pavonina ▴ 150
1
vote
4
replies
2.0k
views
Average depth/coverage before and after PCR duplicates cleanup
markduplicates samtools meandepth BAM
updated 4.0 years ago by 20 • written 4.1 years ago by ▴ 150
0
votes
0
replies
671
views
Blast2gff index issue
gff blastn blast2gff index
4.0 years ago by Begonia_pavonina ▴ 150
4
votes
9
replies
9.1k
views
bcftools consensus command
vcf bcftools
updated 14 months ago by 43k • written 4.3 years ago by ▴ 150
13
votes
6
replies
4.0k
views
bcftools isec -n operators
bcftools intersect
updated 2.7 years ago by 43k • written 4.3 years ago by ▴ 150
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