scATACseq data are very sparse. It is sparser than scRNAseq. To do clustering of scATACseq data, there are some preprocessing steps need to be done.
I want to reproduce what has been done after reading the method section of these two recent scATACseq paper:
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility Darren et.al Cell 2018 Latent Semantic Indexing Cluster Analysis In order to get an initial sense of the relationship between individual cells, we first broke the genome into 5kb windows and then scored each cell for any insertions in these windows, generating a large, sparse, binary matrix of 5kb windows by cells for each tissue.
I want to split the PBMC scATAC bam from 10x by cluster id. So, I can then make a bigwig for each cluster to visualize in IGV.
The first thing I did was googling to see if anyone has written such a tool (Do not reinvent the wheels!). People have done that because I saw figures from the scATAC papers. I just could not find it. Maybe I need to refine my googling skills.
I need a transcript to gene mapping file for Salmon. I am aware of annotation bioconductor packages that can do this job. However, I was working on a species which does not have the annotation in a package format (I am going to use Drosphila as an example for this blog post). I had to go and got the gtf file and made such a file from scratch.
Please read the specifications of those two file formats.