From 170a001729326564e350dc6ee4cf79624345dc5f Mon Sep 17 00:00:00 2001 From: Jos van Nijnatten Date: Mon, 15 Feb 2021 12:54:31 +0100 Subject: [PATCH] Count reads in X and Y chromosome. --- rnaseq/step6_overall_QC/02 - Gender Check.R | 2 ++ 1 file changed, 2 insertions(+) diff --git a/rnaseq/step6_overall_QC/02 - Gender Check.R b/rnaseq/step6_overall_QC/02 - Gender Check.R index f02f19d..92f4e4d 100644 --- a/rnaseq/step6_overall_QC/02 - Gender Check.R +++ b/rnaseq/step6_overall_QC/02 - Gender Check.R @@ -107,4 +107,6 @@ gender.qc.genes.to.plot <- gender.qc.results %>% # - Plot the normalized expressino values for the genes in gender.qc.genes.to.plot in a boxplot, split and colored by gender. # - (Optional) Do a GSVA with as genesets the genes found in gender.qc.genes.to.plot. Plot the boxplots as per the previous point. # - (Optional) Plot the number of Y-chromosome reads devided by the number of X chromosome reads in a boxplot as per the first point. +# x=$(samtools view -q 20 -f 2 $bam_file X | wc -l) +# y=$(samtools view -q 20 -f 2 $bam_file Y | wc -l) # - (Optional) Plot the number of Y-chromosome SNPs devided by the number of X chromosome SNPs in a boxplot as per the first point.