Bi-parental graph ASE analyzer
This python pakage was devised to analyze hybrid RNA-seq using bi-parental graph strategy.
version: 0.1.2
author: Yi Jiang ([email protected]); Muran Yi; Zhule Liu
Mummer4 :4.0.0rc1 or higher
Hisat2 :2.2.1 or higher
Samtools :1.18 or higher
Bedtools :2.31.1 or higher
pip install BigphASE
BigphASEtools [-options] <parent_A genome sequence fa> <parent_B genome sequence fa> <parent_A genome gff3> <clean RNAseq R1 fastq> <clean RNAseq R2 fastq> <prefix>
(1) Graph builder Graph genome was built using one parental genome as backbone, with variations between two parental genomes as alternate paths. (2) RNAseq mapping Clean RNA-seq data were mapped to graph index. (3) ASE genes analysis After mapping, reads were assigned to parental origin based on their genotypes at SNP sites, then maternal and paternal origin reads count of each gene were summed.
