Vcf file based tsne analysis
Hi, I just wonder anyone here has experience of using vcf files (from stacks) to do t-sne analysis? any help would be great.
regards, Shri
vcf
tsne
• 694 views
•
link
written
by
Shripathi •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
ROSE analysis is empty
written by pb11 •I am trying to do ROSE analysis using H3K27ac data. After running the analysis, I am not getting any data. The folders are empty and …
-
working piRNA prediction tools
written by Shripathi •Hi, I found quite a few piRNA prediction tools. However it seems like most of them dont exist anymore or their online links don't work …
-
Signals of selection in RADseq with no population structure?
written by Natasha •Hi everyone, I'm a masters student undertaking my research project with RAD-seq data from three species of bumblebee each taken at four different sites. I …
-
Polyploidy found, and not supported by vcftools for a diploid data set.
written by Shripathi •Hi, I used gatk mutect2-select variant (retained only SNPs)-combinegvcfs to generate a vcf file for a diploid species. When I tried to process the vcf …
-
Public Data Set Download
written by karthick.n •Hi, I need disease specific genomic data of more than 50 samples. Is there any way to download the data set from genomic databases? I'm …
-
UMAP vs "rigorous" t-SNE
written by rtrende •I've heard a lot of people discussing UMAP recently as though it has essentially superseded t-SNE for visualizing scRNA-seq data. UMAP is certainly impressive, but …
-
GATK GermlineCNVCaller & PostprocessGermlineCNVCalls
written by rajitz •Hi, I was wondering if anyone here has experience in running GATK GermlineCNVCaller & PostprocessGermlineCNVCalls for calling CNVs in germline samples? The VCF files that …
-
Can Ion Reporter produce md5 checksums?
written by bawan03 •<p>Hi Everyone,</p> <p>I wondered if anyone has any experience of this...</p> <p>We appear to be having recurrent issues with downloading BAM files from our Ion …
-
Why VarScan cannot call variants which appear in 1000genome
written by sxl919 •HI, I am using VarScan for variant calling and I use the bam files from 1000genome as control for my project. I run the bam …
-
fasta as input file : mapping sequences to a genome
written by Shripathi •Hi to all, I have a fasta file having sequences (similar input file for command line blast program) that I extracted from one of Stacks …