snmC-seq2

July 17, 2018 ยท View on GitHub

snmC-seq2 is an improved technique for single nucleus methylome sequencing. The code used for the manuscript is in this repository.

Computing bin/gene level methylation ratio

The scirpt allc2mat.new.py is for calculating bin/gene level methylation ratio. It can be used as

python allc2mat.new.py allc_sample.tsv.gz #cpus regions.bed

It requires the bed file to be sorted, and allc file need to be put in the same directory with allc index file. The output of allc2mat.new.py includes the following two files.

sample_region.mC.txt

each rows is a region from the input bed file

each columns are

  1. mCH basecalls

  2. CH basecalls

  3. mCH/CH ratio

  4. mCG basecalls

  5. CG basecalls

  6. mCG/CG ratio

sample_region.tot.txt

each columns are

  1. sample name

  2. global mCCC basecalls

  3. global CCC basecalls

  4. global mCH basecalls

  5. global CH basecalls

  6. global mCG basecalls

  7. global CG basecalls

  8. global mCCC/CCC ratio

  9. global mCH/CH ratio

  10. global mCG/CG ratio

Clustering and visualization

Code for clustering and visualization of gene level mCH ratio is in analysis.py, which takes the cell x bin/gene matrix of methylation level as input.