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4
votes
7
replies
457
views
Currently recommended Oxford Nanopore data basecalling and preprocessing pipeline for de novo assembly applications
ONT assembly Nanopore preprocessing basecalling
21 days ago by Denis ▴ 310
2
votes
1
reply
679
views
Proper Bowtie2 settings for snp calling applications
Illumina SNP Freebayes Bowtie2
updated 16 months ago by 44k • written 16 months ago by ▴ 310
5
votes
3
replies
1.1k
views
Illumina reads preprocessing best practice for snp calling applications
Illumina snp
updated 7 months ago by • 0 • written 16 months ago by ▴ 310
0
votes
0
replies
445
views
Correct tRNA genes nomenclature in plant chloroplast genomes
chloroplast tRNA genes genome
18 months ago by Denis ▴ 310
0
votes
0
replies
547
views
Clade model C of PAML to detect positive selection in coding nucleotide sequences
selection evolution PAML CDS
21 months ago by Denis ▴ 310
0
votes
0
replies
503
views
Application of the branch, site and branch-site models for detecting selection with codeml (PAML)
evolution codeml PAML
22 months ago by Denis ▴ 310
0
votes
0
replies
378
views
Alternatives to DendroCypher tool for large trees labeling
selection PAML codeml pressure
22 months ago by Denis ▴ 310
3
votes
3
replies
1.3k
views
Phylogeny inference on complete chloroplast genomes with IQ-TREE software
IQ-TREE genomics phylogenetics
updated 23 months ago by ★ 1.4k • written 23 months ago by ▴ 310
11
votes
6
replies
8.2k
views
6 follow
Making nice plots based on the different metrics from VCF file
snp R genome
updated 2.0 years ago by ▴ 290 • written 6.0 years ago by ▴ 310
6
votes
2
replies
798
views
Advanced search for the sequences on NCBI website
GenBank NCBI
2.3 years ago by Denis ▴ 310
0
votes
0
replies
487
views
Filter out individuals of the multisample VCF file with a high proportion of missing calls by bcftools
SNP VCF missing_data genotyping
2.8 years ago by Denis ▴ 310
0
votes
0
replies
574
views
Mapping of tag sequences to the reference genome in Tassel 5 GBS v2 Pipeline
genotyping Genotyping-by-sequencing Tassel Tassel_GBS_Pipeline bowtie2
2.9 years ago by Denis ▴ 310
2
votes
1
reply
709
views
Get rid of multimapped and unmapped reads for snp calling improvement
genome mapping SNP Illumina
updated 2.9 years ago by 85k • written 2.9 years ago by ▴ 310
0
votes
0
replies
727
views
Does the SOAP (BGI) website mirror exist
software SOAP
updated 3.1 years ago by • 0 • written 3.2 years ago by ▴ 310
2
votes
2
replies
1.2k
views
Understandig of some bbmerge command line settings
software amplicons bbmerge
3.2 years ago by Denis ▴ 310
6
votes
7
replies
3.6k
views
Primers trimming from Illumina paired-end reads by BBDuk software
Illumina adapter BBDuk trimming amplicons PCR
updated 3.2 years ago by 147k • written 3.2 years ago by ▴ 310
0
votes
0
replies
511
views
Reads preparation steps for amplicon metagenomics
PCR Metagenomics
3.2 years ago by Denis ▴ 310
3
votes
2
replies
758
views
Is removing of the one trailing nucleotide in Illumina reads necessary step of data preprocessing
Illumina Preprocessing
3.5 years ago by Denis ▴ 310
6
votes
3
replies
9.7k
views
The fastest way to download a list of SRR accessions from Sequence Read Archive with sratoolkit
sequence genome
updated 3.7 years ago by ▴ 20 • written 4.9 years ago by ▴ 310
6
votes
2
replies
1.4k
views
Using DESeq2 for DE analysis of microRNA data
RNA-Seq R
3.9 years ago by Denis ▴ 310
5
votes
5
replies
2.2k
views
Merge overlapping and adjacent features in the BED file having the same label in the name (4-th) column
genome R
updated 4.0 years ago by 36k • written 4.0 years ago by ▴ 310
0
votes
0
replies
737
views
Circos could not open image.conf error
software error
4.1 years ago by Denis ▴ 310
0
votes
6
replies
1.5k
views
Running Mauve on circular genomes
genome alignment
4.1 years ago by Denis ▴ 310
2
votes
5
replies
2.6k
views
Prefetch error while downloading data from sequence read archive
software error
4.7 years ago by Denis ▴ 310
6
votes
6
replies
4.3k
views
Aspera ascp command line utility inside prefetch call to facilitate SRA data downloading
genome next-gen
4.7 years ago by Denis ▴ 310
0
votes
0
replies
1.4k
views
RNA editing sites prediction in plant mitogenome without rna-seq data
rna editing
updated 4.9 years ago by 20 • written 7.6 years ago by ▴ 310
2
votes
2
replies
633
views
Frontmost snp callers for plant genomes
alignment next-gen SNP genome
updated 5.1 years ago by 13k • written 5.1 years ago by ▴ 310
3
votes
5
replies
1.2k
views
Good questions and answers resources (forums) on Ecology and Statistics
ecology
updated 5.3 years ago by ▴ 180 • written 5.3 years ago by ▴ 310
1
vote
0
replies
1.0k
views
Understanding of fields meaning in HapMap.hmc.txt file from UNEAK pipeline in Tassel 3.0
sequencing genome SNP
5.3 years ago by Denis ▴ 310
1
vote
1
reply
775
views
Minimal requirements for the draft genome assembly
genome assembly sequence
updated 5.3 years ago by 44k • written 5.3 years ago by ▴ 310
2
votes
3
replies
1.1k
views
Mapping Phred+64 encoded reads with Bowtie2
genome alignment software error
updated 5.4 years ago by 20 • written 5.5 years ago by ▴ 310
2
votes
3
replies
4.7k
views
Canonical Correspondence Analysis in R with Vegan library
R
updated 5.4 years ago by 27k • written 5.4 years ago by ▴ 310
7
votes
4
replies
6.7k
views
Bootstrap values on the phylogenetic tree in Ape r package
R phylogenetics
5.4 years ago by Denis ▴ 310
7
votes
3
replies
3.8k
views
Calculate distance matrix from nucleotide alignment with multiple IUPAC ambiguity characters
alignment sequence phylogenetics
updated 5.5 years ago by ▴ 160 • written 5.6 years ago by ▴ 310
6
votes
8
replies
2.8k
views
Unexpected Bowtie2 behavior with --phred64 and --phred33 flags
software error alignment
updated 2.8 years ago by 104k • written 5.5 years ago by ▴ 310
1
vote
1
reply
3.0k
views
Interpretation of Tassel MLM output
SNP genome GWAS
6.1 years ago by Denis ▴ 310
0
votes
0
replies
1.1k
views
Calculate a square matrix of r2 between all SNPs in genome during LD analysis
SNP genome R
6.1 years ago by Denis ▴ 310
13
votes
13
replies
8.0k
views
6 follow
Extract SNPs flanking sequences based on VCF and genome Fasta files
snp sequence genome
updated 15 months ago by • 0 • written 6.3 years ago by ▴ 310
12
votes
1
reply
5.6k
views
Extract SNPs from VCFfile located in genes based on GFF file information
gene snp
updated 6.3 years ago by 16k • written 6.3 years ago by ▴ 310
6
votes
2
replies
1.9k
views
A way to verify that GFF and Fasta files make a valid pair (came from the same project version)
assembly genome
6.3 years ago by Denis ▴ 310
2
votes
4
replies
2.0k
views
Multiple testing correction in linear mixed models (MLM) for GWAS
GWAS
updated 6.3 years ago by ▴ 280 • written 6.3 years ago by ▴ 310
5
votes
11
replies
3.6k
views
Different samples order in .ped and phynotype data files
Plink GWAS R
6.3 years ago by Denis ▴ 310
7
votes
8
replies
3.6k
views
Number of bases with a certain quality in FASTQ file
next-gen sequencing
updated 6.4 years ago by 35k • written 6.4 years ago by ▴ 310
10
votes
16
replies
4.7k
views
Demultiplexing of the Illumina PE data
next-gen sequencing
updated 6.4 years ago by 147k • written 6.4 years ago by ▴ 310
0
votes
0
replies
943
views
Clustering 454 amplicon data
next-gen sequencing SNP
6.5 years ago by Denis ▴ 310
4
votes
2
replies
5.2k
views
Convert blast tabular output to bed format
genome
6.5 years ago by Denis ▴ 310
0
votes
0
replies
1.0k
views
Minimal pool size for extreme qtl approach in plants
SNP GWAS QTL genome
6.6 years ago by Denis ▴ 310
2
votes
2
replies
2.7k
views
Analysis of paired-end GBS data
next-gen SNP genome
6.9 years ago by Denis ▴ 310
1
vote
0
replies
2.9k
views
Understanding Best-Hits filtering algorithm in BLAST+ applications
blast alignment
updated 7.0 years ago by 44k • written 7.0 years ago by ▴ 310
7
votes
12
replies
2.8k
views
Optimization of RNA-Seq data mapping with tophat2
RNA-Seq alignment
updated 7.3 years ago by ★ 1.6k • written 7.3 years ago by ▴ 310
55 results • Page 1 of 2
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