This repository contains Python scripts for allele-specific mapping. They were used to map ATAC-seq, RNA-seq and Hi-C reads in a mouse hybrid cell line to study the reactivation kinetics of the X chromosome during iPS cell reprogramming. However, the scripts are general and they can be used for other purposes.
The code requires only a standard computer with enough RAM to support the in-memory operations.
This code is supported for Linux. The package has been tested on the following systems:
- Linux: Ubuntu 14.04.6
- Scientific Linux 7.2
The code is written for Python 2.7 or 3.7 and does not depend on additional packages.
git clone https://github.com/gui11aume/asmap
Downloading the files is sufficient and there is no further requirement to install the software.
To run the demo, set the current directory to asmap/demo. Assuming that you just downloaded
the repository from Github, run:
cd asmap/demo
Then you need to run the script merge_assign.py on the two SAM files of dummy ATAC-seq reads
mapped in Mus musculus castaneus and in Mus musculus musculus, and on the p2f files that
contain the information to lift over the coordinates from the genomes of castaneus and musculus
to the mouse reference genome (mm10). You can do this with the following command:
python ../merge_assign.py mapped_in_cas.sam mapped_in_mus.sam p2f/* > disambiguated_no_header.sam
The running time should be less than 1 minute. The command creates a SAM file without header where
the reads are assigned to one genome or the other. The chromosomes now have the suffix .ref and
the coordinates are expressed in the reference genome (mm10).
Every line of the SAM file contains an additional field labelled ZZ:Z: that
contains the final call for every read. The values in this demo are chrX.cas if the read is
assigned to the castaneus genome; chrX.mus if it is assigned to the musculus genome; amb if
there is an ambiguity between two unique sites of the castaneus and musculus genome; and rep
if there is an ambiguity between several repeated sites of each genome.
To run the software on your data, you must first map the reads of interest with
BWA MEM (an example Makefile is provided). The reads must be mapped
separately in both genomes of interest. It is important that the chromosomes in the two genomes
have the same name with different suffixes (e.g., chrX.cas and chrX.mus).
The reads can be disambiguated using the same command as in the demo. If p2f files are provided,
the coordonates will be shifted to the corresponding reference. Othewise, they will be set as
nan.
This project is in the public domain.