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5
votes
2
replies
182
views
Advanced search for the sequences on NCBI website
GenBank NCBI
2 days ago by Denis ▴ 230
0
votes
0
replies
168
views
Filter out individuals of the multisample VCF file with a high proportion of missing calls by bcftools
SNP VCF missing_data genotyping
5 months ago by Denis ▴ 230
0
votes
0
replies
173
views
Mapping of tag sequences to the reference genome in Tassel 5 GBS v2 Pipeline
genotyping Genotyping-by-sequencing Tassel Tassel_GBS_Pipeline bowtie2
6 months ago by Denis ▴ 230
2
votes
1
reply
290
views
Get rid of multimapped and unmapped reads for snp calling improvement
genome mapping SNP Illumina
updated 7 months ago by 64k • written 7 months ago by ▴ 230
0
votes
0
replies
379
views
Does the SOAP (BGI) website mirror exist
software SOAP
updated 9 months ago by • 0 • written 10 months ago by ▴ 230
2
votes
2
replies
561
views
Understandig of some bbmerge command line settings
software amplicons bbmerge
10 months ago by Denis ▴ 230
5
votes
7
replies
1.3k
views
Primers trimming from Illumina paired-end reads by BBDuk software
Illumina adapter BBDuk trimming amplicons PCR
updated 10 months ago by 118k • written 10 months ago by ▴ 230
0
votes
0
replies
215
views
Reads preparation steps for amplicon metagenomics
PCR Metagenomics
10 months ago by Denis ▴ 230
3
votes
2
replies
356
views
Is removing of the one trailing nucleotide in Illumina reads necessary step of data preprocessing
Illumina Preprocessing
14 months ago by Denis ▴ 230
5
votes
3
replies
4.5k
views
The fastest way to download a list of SRR accessions from Sequence Read Archive with sratoolkit
sequence genome
updated 16 months ago by ▴ 10 • written 2.6 years ago by ▴ 230
3
votes
2
replies
709
views
Using DESeq2 for DE analysis of microRNA data
RNA-Seq R
19 months ago by Denis ▴ 230
5
votes
5
replies
1.1k
views
Merge overlapping and adjacent features in the BED file having the same label in the name (4-th) column
genome R
updated 20 months ago by 34k • written 20 months ago by ▴ 230
0
votes
0
replies
394
views
Circos could not open image.conf error
software error
21 months ago by Denis ▴ 230
0
votes
6
replies
685
views
Running Mauve on circular genomes
genome alignment
21 months ago by Denis ▴ 230
2
votes
5
replies
1.6k
views
Prefetch error while downloading data from sequence read archive
software error
2.4 years ago by Denis ▴ 230
6
votes
6
replies
2.9k
views
Aspera ascp command line utility inside prefetch call to facilitate SRA data downloading
genome next-gen
2.4 years ago by Denis ▴ 230
0
votes
0
replies
1.1k
views
RNA editing sites prediction in plant mitogenome without rna-seq data
rna editing
updated 2.6 years ago by 20 • written 5.3 years ago by ▴ 230
2
votes
2
replies
374
views
Frontmost snp callers for plant genomes
alignment next-gen SNP genome
updated 2.8 years ago by 13k • written 2.8 years ago by ▴ 230
9
votes
5
replies
4.1k
views
Making nice plots based on the different metrics from VCF file
snp R genome
updated 2.8 years ago by ★ 2.1k • written 3.7 years ago by ▴ 230
3
votes
5
replies
542
views
Good questions and answers resources (forums) on Ecology and Statistics
ecology
updated 3.0 years ago by ▴ 170 • written 3.0 years ago by ▴ 230
0
votes
0
replies
676
views
Understanding of fields meaning in HapMap.hmc.txt file from UNEAK pipeline in Tassel 3.0
sequencing genome SNP
3.0 years ago by Denis ▴ 230
1
vote
1
reply
510
views
Minimal requirements for the draft genome assembly
genome assembly sequence
updated 3.0 years ago by 36k • written 3.0 years ago by ▴ 230
2
votes
3
replies
702
views
Mapping Phred+64 encoded reads with Bowtie2
genome alignment software error
updated 3.0 years ago by 20 • written 3.2 years ago by ▴ 230
2
votes
3
replies
3.5k
views
Canonical Correspondence Analysis in R with Vegan library
R
updated 3.0 years ago by 26k • written 3.0 years ago by ▴ 230
7
votes
4
replies
4.3k
views
Bootstrap values on the phylogenetic tree in Ape r package
R phylogenetics
3.1 years ago by Denis ▴ 230
7
votes
3
replies
2.7k
views
Calculate distance matrix from nucleotide alignment with multiple IUPAC ambiguity characters
alignment sequence phylogenetics
updated 3.2 years ago by ▴ 140 • written 3.2 years ago by ▴ 230
6
votes
8
replies
1.5k
views
Unexpected Bowtie2 behavior with --phred64 and --phred33 flags
software error alignment
updated 6 months ago by 102k • written 3.2 years ago by ▴ 230
1
vote
1
reply
2.0k
views
Interpretation of Tassel MLM output
SNP genome GWAS
3.7 years ago by Denis ▴ 230
0
votes
0
replies
884
views
Calculate a square matrix of r2 between all SNPs in genome during LD analysis
SNP genome R
3.8 years ago by Denis ▴ 230
12
votes
12
replies
4.7k
views
Extract SNPs flanking sequences based on VCF and genome Fasta files
snp sequence genome
updated 4.0 years ago by 147k • written 4.0 years ago by ▴ 230
11
votes
1
reply
4.0k
views
Extract SNPs from VCFfile located in genes based on GFF file information
gene snp
updated 4.0 years ago by 15k • written 4.0 years ago by ▴ 230
6
votes
2
replies
1.4k
views
A way to verify that GFF and Fasta files make a valid pair (came from the same project version)
assembly genome
4.0 years ago by Denis ▴ 230
2
votes
4
replies
1.4k
views
Multiple testing correction in linear mixed models (MLM) for GWAS
GWAS
updated 4.0 years ago by ▴ 280 • written 4.0 years ago by ▴ 230
5
votes
11
replies
2.0k
views
Different samples order in .ped and phynotype data files
Plink GWAS R
4.0 years ago by Denis ▴ 230
7
votes
8
replies
1.9k
views
Number of bases with a certain quality in FASTQ file
next-gen sequencing
updated 4.1 years ago by 34k • written 4.1 years ago by ▴ 230
10
votes
16
replies
2.9k
views
Demultiplexing of the Illumina PE data
next-gen sequencing
updated 4.1 years ago by 118k • written 4.1 years ago by ▴ 230
0
votes
0
replies
683
views
Clustering 454 amplicon data
next-gen sequencing SNP
4.2 years ago by Denis ▴ 230
4
votes
2
replies
3.3k
views
Convert blast tabular output to bed format
genome
4.2 years ago by Denis ▴ 230
0
votes
0
replies
722
views
Minimal pool size for extreme qtl approach in plants
SNP GWAS QTL genome
4.3 years ago by Denis ▴ 230
1
vote
2
replies
2.1k
views
Analysis of paired-end GBS data
next-gen SNP genome
4.5 years ago by Denis ▴ 230
1
vote
0
replies
2.2k
views
Understanding Best-Hits filtering algorithm in BLAST+ applications
blast alignment
updated 4.7 years ago by 36k • written 4.7 years ago by ▴ 230
7
votes
12
replies
1.9k
views
Optimization of RNA-Seq data mapping with tophat2
RNA-Seq alignment
updated 4.9 years ago by ★ 1.6k • written 4.9 years ago by ▴ 230
3
votes
2
replies
2.5k
views
Software to in silico test restriction enzymes for GBS sequencing and similar approaches
next-gen SNP genome sequencing
updated 5.1 years ago by 34k • written 5.1 years ago by ▴ 230
0
votes
0
replies
908
views
Orthologs search in plant plastid genomes
genome gene blast alignment
5.2 years ago by Denis ▴ 230
5
votes
2
replies
968
views
A question about blast algorithm
alignment blast
updated 5.2 years ago by 5.6k • written 5.2 years ago by ▴ 230
1
vote
1
reply
1.1k
views
Metrics to compare different tools for PE reads merging
next-gen
5.8 years ago by Denis ▴ 230
1
vote
3
replies
1.3k
views
Most accurate way to measure adapters quantity in NGS illumina reads
next-gen
updated 5.8 years ago by ★ 2.4k • written 5.8 years ago by ▴ 230
47 results • Page 1 of 1
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