GRanges

TSS enrichment score serves as an important quality control metric for ATACseq data. I want to write a script for single cell ATACseq data. From the Encode page: Transcription Start Site (TSS) Enrichment Score - The TSS enrichment calculation is a signal to noise calculation. The reads around a reference set of TSSs are collected to form an aggregate distribution of reads centered on the TSSs and extending to 1000 bp in either direction (for a total of 2000bp).

This post was inspired by Andrew Hill’s recent blog post. Inspired by some nice posts by @timoast and @tangming2005 and work from @10xGenomics. Would still definitely have to split BAM files for other tasks, so easy to use tools for that are super useful too! — Andrew J Hill (@ahill_tweets) April 13, 2019 Andrew wrote that blog post in light of my other recent blog post and Tim’s (developer of the almighty Seurat package) blog post.

Googling is a required technique for programmers. Once I have a programming problem in mind, the first thing I do is to google to see if other people have encountered the same problem and maybe they already have a solution. Do not re-invent the wheels. Actually, reading other people’s code and mimicing their code is a great way of learning. Today, I am going to show you how to compute binned averages/sums along a genome or any genomic regions of interest.

You might want to use the bedtools for solutions. see Dave Tang’s post.

When structural variants are represented in bedpe format, each structural variant is represented as two linked breakpoints. Each breakpoint is represented…

Make sure you read my note for the “+” and “-” strandness of bedpe for structural variants. In a word, + means the region is at the 5’ of the breakpoint and…