Tag: chrX

Tools for Normalizing and Comparing ChIP-seq Samples

data(H3K27Ac, package = “MAnorm2”) attr(H3K27Ac, “metaInfo”) ## Make a comparison between GM12891 and GM12892 cell lines and create an MA ## plot on the comparison results. # Perform MA normalization and construct bioConds to represent the two cell # lines. norm <- normalize(H3K27Ac, 5:6, 10:11) norm <- normalize(norm, 7:8, 12:13)…

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Produce PCA bi-plot for 1000 Genomes Phase III

Note1 – Previous version: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old) Note2 – this data is for hg19 / GRCh37 Note3 – GRCh38 data is available HERE The tutorial has been updated based on the 1000 Genomes Phase III imputed genotypes. The original tutorial was…

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MAPQ (Mapping quality) of 0 for most reads from BWA-MEM2 (with no secondary alignment or other apparent reason)

Hello, I got a very weird output from BWA-mem2 – most of the reads have mapping quality of 0, even though there is no secondary alignment or anything else suspicious. I got sequencing data that was aligned with Novoalign to hg18, the data was bam files. I needed to realign…

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Transcription Factor Functions

Transcription Factor Functions 1 I have been wondering if there is a database that contains information about whether a transcription factor has a repressive or an activating or a context-dependent function. factor database transcription • 71 views If you performed a whole-genome FIMO scan, selecting those hits that match your…

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Fasta.fai file error

Fasta.fai file error 0 Hi, I have been struggling with an error in bedtools intersect. The command I am trying to run is as follows bedtools intersect -a sorted.vcf -b nstd166.GRCh38.variant_call_chr.vcf.gz -wo -sorted -f 0.8 -r -g Homo_sapiens_assembly38.fasta.fai For some of the files that I am assessing, I don’t get…

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What is the difference between GRCh37 and hs37? And hg19?

This is what I have found so far. Please correct me if I am wrong. GRCh37 w/o patches includes the primary assembly (22 autosomal, X. Y, and non-chromosomal supecontigs) and alternate scaffolds, but not a reference mitogenome. Non-chromosomal supercontigs are the unlocalized and unplaced scaffolds. The rCRS reference mitogenome in…

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To find total genes on favorable chromosome

To find total genes on favorable chromosome 2 How can I find how many genes exist on each chromosome? genes total • 52 views Counting from GENCODE for the vM27 mouse reference: wget ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M27/gencode.vM27.annotation.gtf.gz #/ In R: library(rtracklayer) gtf <- rtracklayer::import(“~/gencode.vM27.annotation.gtf.gz”) table(as.character(seqnames(gtf[gtf$type==”gene”]))) chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16…

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Platypus

Platypus 0 Hi, I’m super new to WGS and bioinformatics, but I’m a classic software data scientist, so I know enough to be annoying. I’m using Platypus too call variants on 100X WGS via Nebula Genomics. I found an odd series of calls and am not sure if this is…

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gender determination and chrX CN calls

gender determination and chrX CN calls 1 I’m running CNVKit in amplicon mode on a set of tumor bam files generated with a small amplicon panel of 45 genes. The panel includes just one gene on chrX, and none on chrY. My reference is generated by 10 normal male samples…

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Default CNV call thresholds for haplotype chromosome s

Default CNV call thresholds for haplotype chromosome s 0 Hi, I confuse a topic that about the CNV call. The default thresholds are -1.1 => 0, -0.25 => 1, 0.2 => 2, 0.7 => 3 for discrete copy number. But these thresholds doesn’t work for chrY and chrX. What is…

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