User: dominicdhall

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dominicdhall40
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Posts by dominicdhall

<prev • 10 results • page 1 of 1 • next >
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Probabilistic PCA on very sparse SNP matrix
... I have a very sparse SNP matrix (~90% missing genotypes by sample and ~90% missing samples per SNP) which I would like to perform some sort of probabilistic PCA on. I have been using the packages VariantAnnotation to get the my snpMatrix object and originally tried to mimic a method shown here (http ...
probabilistic pca pca snpstats snpmatrix written 18 months ago by dominicdhall40 • updated 15 months ago by Biostar ♦♦ 20
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PCA and statistics on SNPmatrix
... I have a VCF file containing genotype date for a few thousand SNPs across a few thousand samples. I would like to firstly convert this to a matrix (possibly using the VariantAnnotation package) and then perform a PCA analysis on the samples followed by some sort of clustering algorithm. I have very ...
pca snp written 18 months ago by dominicdhall40 • updated 18 months ago by leeandroid90
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Comment: C: Creating a cell by SNP matrix
... I did consider merging my VCF files using each cell as a separate sample. Do you know if this would allow me to perform subsequent dimensionality reduction and clustering? Or would the data have to be loaded into some sort of dataframe first? (I apologise I am very new to bioinformatics in general.. ...
written 18 months ago by dominicdhall40
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Comment: C: Creating a cell by SNP matrix
... Honestly I am unsure! I think the nature of the variant isn't too important, only that it has a label. Then for each (barcode, SNP label) pair I would either have a 0, 1 or 2. 0 would be homozygous reference, 1 would be heterozygous and 2 would be homozygous alternative allele (sorry if these labels ...
written 18 months ago by dominicdhall40
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Creating a cell by SNP matrix
... In a recent experiment with a few thousand barcoded cells I wanted to investigate common SNPs. I have a large .bam file consisting of all reads from all cells which passed quality control for which I have run variant calling and subsequent QC on the called variants - this was saved in `calls.vcf`(th ...
variant calling bcftools snp genotyping written 18 months ago by dominicdhall40 • updated 6 months ago by niklas.lang20
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Comment: A: Creating a Zebrafish reference genome for use by mpileup
... I will give a try just having the chromosome number - however, how will mpileup know where these variants actually lie if it just has the chromosome and sequence? Does it work out it out? As for the comment - sorry that is very ambiguous from me. It is essentially just because i couldnt remember e ...
written 19 months ago by dominicdhall40
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Answer: A: How I can change many names of list file
... I think you can use: for file in *.adjust do mv -i "${file}" "${file/.adjust/}" done (Assuming they aren't in a txt file - in which case the given answer works a treat) ...
written 19 months ago by dominicdhall40
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Creating a Zebrafish reference genome for use by mpileup
... I'm trying to download an appropriate reference genome for use in reference calling a bunch of reads I have for zebrafish. The reads I have are from the 10x platform looking at single cell RNA transcripts. Currently I have a BAM file and would like to create a vcf file of variant sites within my rea ...
vcf variant calling faidx rna-seq mpileup written 19 months ago by dominicdhall40
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Comment: C: de novo variant SNP calling from barcoded single-cell data
... I didn't produce the data set but I have been assured that there is the necessary depth to work out a sample of variant SNPs present within each cell. ...
written 19 months ago by dominicdhall40
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de novo variant SNP calling from barcoded single-cell data
... I have a BAM file containing sorted, aligned reads from a number of single cells. Each read has an associated cell barcode (CB tag). I would like to consider all aligned reads and produce a VCF file of SNP variants from my single cell data. I have looked over the documentation for `bcftools mpileup` ...
vcf single-cell rna-seq written 19 months ago by dominicdhall40 • updated 6 months ago by niklas.lang20

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