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Showing top results for tag: Stacks • reset
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News: RADseq data analysis using Stacks (online course)
RADseq Phylogenomics Population-Genomics Stacks
updated 29 days ago by 44k • written 29 days ago by ★ 2.6k
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0
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250
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ddRADseq: GATK not matching STACKS refmap in terms of resolution?
polyploidy RADseq variant-calling STACKS GATK
updated 3 months ago by 44k • written 3 months ago by • 0
0
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0
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172
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News: Course: RADseq data analysis using Stacks (online)
RAD-seq Genomics Stacks Phylogenomics Population
updated 3 months ago by 44k • written 3 months ago by ★ 2.6k
1
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2
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522
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STACKS PCR duplicate removal
PCR VCF STACKS RAD-seq
7 months ago by maxrwjones ▴ 60
0
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0
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278
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Parsing error when using sstacks
stacks sstacks
updated 9 months ago by 44k • written 9 months ago by ▴ 40
1
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1
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426
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stacks . vcf . admixture , structure extract data from vcf ?
radseq stacks structure
updated 10 months ago by 164k • written 10 months ago by • 0
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0
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495
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News: RADseq data analysis course
RADseq Phylogenomics Stacks Population-Genomics
12 months ago by carlopecoraro2 ★ 2.6k
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2
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1.1k
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News: The Practice of RADseq: Population Genomics Analysis with Stacks (RADS02) Early bird deadline approaching - 20th September
population-genomics radseq stacks
updated 13 months ago by ★ 1.9k • written 13 months ago by ▴ 110
0
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1
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695
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Stacks' populations.sumstats.tsv : interpreting pi for populations with one individual
summary-statistics Stacks pi
updated 14 months ago by 44k • written 14 months ago by • 0
0
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1
reply
468
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error runing population in stacks
stacks
updated 4 months ago by ▴ 130 • written 15 months ago by ▴ 10
1
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3
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688
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path error
script stacks
updated 15 months ago by 164k • written 15 months ago by ▴ 10
0
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0
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577
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News: Course - RADseq data analysis with Stacks
RADseq Phylogenomics Stacks Population-genomics
updated 15 months ago by 44k • written 15 months ago by ★ 2.6k
0
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0
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478
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Problem creating .bed files with plink
.ped .bed STACKS plink vcf
16 months ago by Loïs • 0
1
vote
1
reply
522
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Unexpected break in site frequency spectrum pattern
frequency sfs Stacks site spectrum populations
18 months ago by S ▴ 10
1
vote
2
replies
1.3k
views
stacks ref_map.pl ERROR 128
ref_map stacks filtering BAM VCF
18 months ago by Ale • 0
1
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0
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564
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STACKS pipeline. Confused about paired-end with "ustacks".
STACKS
21 months ago by Roland ▴ 20
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0
replies
649
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Running ADMIXTURE on .ped files
ped bed ADMIXTURE plink Stacks
2.4 years ago by Austin • 0
0
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0
replies
411
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Help with mounting VCF file parameters adenovo
denovo stacks snp vcf asembly
2.4 years ago by Pamella • 0
0
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0
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536
views
News: ONLINE COURSE - RADseq data analysis using Stacks
Phylogenomics Population RADseq Genomics Stacks
2.5 years ago by carlopecoraro2 ★ 2.6k
0
votes
1
reply
543
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Comparing loci across catalogs
Stacks reference alignment RADseq adegenet
updated 17 months ago by • 0 • written 2.5 years ago by • 0
0
votes
1
reply
539
views
How many individuals per SNP?
ddRAD VCF SNPs Stacks
updated 2.5 years ago by ▴ 280 • written 2.5 years ago by • 0
2
votes
2
replies
821
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Problem with vcf file columns
stacks vcf
updated 3.0 years ago by 164k • written 3.0 years ago by ▴ 40
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0
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618
views
no restriction enzyme in process_radtags
process_radtags restriction stacks enzyme
3.0 years ago by strive • 0
0
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0
replies
1.1k
views
Memory issue with my PC when trying to convert PLINK to TreeMix
STACKS bash vcf plink treemix
3.5 years ago by hemr3 ▴ 10
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0
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725
views
Alternative free software for recombination rate estimation ?
radseq joinmap stacks
3.5 years ago by Picasa ▴ 650
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0
replies
536
views
Strange gstacks warning
stacks gstacks
3.6 years ago by mcrepeau ▴ 20
0
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0
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657
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How many GBS derived reads pass filters after demultiplexing, adapter removal, trimming and filtering?
GBS SNP Stacks Cutadapt
3.6 years ago by giulia.trauzzi ▴ 30
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0
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698
views
Stacks: Denovo.pl M, m and n paramters
Assembly SNP RAD-Seq Stacks
3.7 years ago by virtualinterlect • 0
0
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2
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873
views
Stacks 1.44 Error
RAD-Seq ddRAD Stacks
updated 3.7 years ago by 35k • written 3.7 years ago by • 0
0
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0
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559
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RADseq processing parameters vs. data quality
Stacks RADseq assembly
updated 3.8 years ago by 20 • written 3.8 years ago by • 0
0
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5
replies
2.2k
views
How to strip barcodes from demultiplexed data
stacks
updated 3.8 years ago by 146k • written 3.8 years ago by ▴ 20
0
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0
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924
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News: Training - RADseq data analysis
SNP RADseq Stacks
updated 17 months ago by 44k • written 4.3 years ago by ★ 2.6k
2
votes
1
reply
1.7k
views
Tutorial STACKS ddRADseq
STACKS ddRADseq
updated 4.3 years ago by 146k • written 4.3 years ago by ▴ 350
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2
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1.5k
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LOSITAN only recognising one loci from STACKS genepop file
lositan outlier stacks
updated 5.1 years ago by • 0 • written 7.2 years ago by • 0
0
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0
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1.2k
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News: 5 PART-FUNDED SCHOLARSHIPS for the course "The Practice of RADseq: Population Genomics Analysis with Stacks (RDSQ01)"
Genomics RAD-Seq Stacks
updated 17 months ago by 44k • written 5.3 years ago by ▴ 60
4
votes
5
replies
2.7k
views
Allele frequency visualization
snp R stacks vcftools
updated 17 months ago by • 0 • written 5.9 years ago by ▴ 80
0
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2
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2.1k
views
How to process degenerate base region (DBRs) in a ddRAD sequencing protocol (remove PCR duplicates)?
ddRAD next-gen Stacks DBR
updated 17 months ago by 44k • written 7.1 years ago by ▴ 600
0
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0
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1.7k
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Extract mitochondrial DNA from paired-end RAD-seq data: bwa and stacks
stacks bwa RAD-SEQ
6.1 years ago by CaffeSospeso ▴ 50
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0
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1.4k
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joinmap output from genotypes program of Stacks
stacks joinmap ddrad linkage mapping
6.4 years ago by jav • 0
0
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0
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2.3k
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stacks denovo output directory can't be read in running genotypes program
stacks genotypes linkage map ddrad joinmap
6.4 years ago by jav • 0
0
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0
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1.0k
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News: Workshop_RAD-seq data analysis in Berlin (2-6 July 2018 )
RADseq SNP Stacks
updated 17 months ago by 44k • written 6.4 years ago by ★ 2.6k
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0
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1.2k
views
News: RAD-seq data analysis course in Berlin
Unix Stacks RAD-seq
updated 17 months ago by 44k • written 6.6 years ago by ★ 2.6k
0
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1
reply
1.7k
views
News: Course: RADseq data analysis in Berlin (4-8/12/17). LAST CALL
STACKs RADseq
updated 17 months ago by 44k • written 7.0 years ago by ★ 2.6k
0
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0
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2.2k
views
News: Course: RADseq data analysis in Berlin (4-8/12/17)
RADseq Stacks
updated 17 months ago by 44k • written 7.0 years ago by ★ 2.6k
0
votes
2
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1.7k
views
error in using stacks pipeline
Assembly stacks ngs
7.2 years ago by shynilasanthi ▴ 40
1
vote
5
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2.1k
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Identify the number of unique fragments from MiSeq data
MiSeq stacks RAD
updated 8.3 years ago by ★ 4.0k • written 8.3 years ago by ▴ 10
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0
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1.9k
views
Anybody use Stacks to study RAD seq data ?
rad seq stacks
8.4 years ago by Picasa ▴ 650
1
vote
2
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3.0k
views
Generating genetic map using the mapping population (GBS data)
GBS linkage-map stacks genetic-map
updated 2.2 years ago by 44k • written 9.0 years ago by ★ 1.9k
2
votes
5
replies
3.9k
views
Tool: Stacks: Pipeline For Building Loci Out Of A Set Of Short-Read Sequenced Samples Of Rad-Seq
Stacks
updated 16 months ago by 44k • written 12.3 years ago by 101k
49 results • Page 1 of 1
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Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by ATpoint 85k
> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect? You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type by conmul • 0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
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Thank you for your answer, it's very inspiring.
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Thanks Pierre, I was actually thinking about the duplicate PCR reads and didn't explain it properly. I have found a post mentioning that qu…
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Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could im…
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The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
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I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
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What do you mean by "significant gene"? How did you perform GSEA and on how did you rank your genes for it? From guesswork I might initiall…
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The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
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Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?
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The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
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any idea, how can I display the labels Pre and POst on the top of the heatmap? I am looking at complexheatmap package as to how they displa…
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What p-value do you mean? When and how did you calculate it?
Answer: What is a genomic range that would almost always get decent WGS coverage but is by i.sudbery 20k
What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
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One of the improvements that the using the `salmon` -> `tximport` -> `DESeq2` pipeline, over just a `counts`->`DESeq2` pipeline is the abil…
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