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Count reads in X and Y chromosome.

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Jos van Nijnatten 2021-02-15 12:54:31 +01:00
parent 648cd09a0e
commit 170a001729
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rnaseq/step6_overall_QC/02 - Gender Check.R
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@ -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.