Allele-specific expressed gene

Allele-Specific Expression Quantification

To quantify allele-specific gene expression based on the LongcallR-phased BAM, run the following command to get output.ase.tsv:

python longcallR-ase.py
-b <phased_bam> 
-a <annotation>
-o <output_prefix>
-t <threads>
--gene_types <gene_types>
--min_support <min_support>

+ -b, --bam: longcallR phased bam file + -a, --annotation: Annotation file GTF for GFF3 format + -o, --output: Prefix of output files + -t, --threads: Number of threads + --gene_types: Gene types to be analyzed. Default: ["protein_coding", "lncRNA"] + --min_support: Minimum support reads for counting event. Default: 10

High-Confidence ASE Using Known Genomic SNPs

To increase confidence by requiring allele-specific expression to be supported by both LongcallR SNPs and known genomic SNPs, use the following command to get output.filter_ase.tsv:

python longcallR-ase.py
-b <phased_bam>
--vcf1 <longcallR_phased_vcf>
--vcf3 <genomic_vcf>
-a <annotation>
-o <output_prefix>
-t <threads>
--gene_types <gene_types>
--min_support <min_support>

+ --vcf1: LongcallR phased vcf file + --vcf3: DNA vcf file

Using Phased Genomic VCF for Parental Allele Resolution

To assign allele-specific expression to paternal and maternal haplotypes, provide both the LongcallR-phased VCF and a whole-genome haplotype-phased DNA VCF, get output.patmat_ase.tsv:

python longcallR-ase.py
-b <phased_bam>
--vcf1 <longcallR_phased_vcf>
--vcf2 <phased_genomic_vcf>
-a <annotation>
-o <output_prefix>
-t <threads>
--gene_types <gene_types>
--min_support <min_support>

+ --vcf1: LongcallR phased vcf file + --vcf2: Whole genome haplotype phased DNA vcf file

Output format

1.output.ase.tsv or output.filter_ase.tsv

Column	Description
`#Gene_name`	Gene symbol
`Chr`	Chromosome
`PS`	Phase set ID
`H1`	Read count assigned to haplotype 1
`H2`	Read count assigned to haplotype 2
`P_value`	Binomial test p-value for allelic imbalance

2.output.patmat_ase.tsv

Column	Description
`#Gene_name`	Gene symbol
`Chr`	Chromosome
`PS`	Phase set ID
`H1`	Read count assigned to haplotype 1
`H2`	Read count assigned to haplotype 2
`P_value`	Binomial test p-value for allelic imbalance
`H1_Paternal`	Read count in H1 supporting the paternal allele
`H1_Maternal`	Read count in H1 supporting the maternal allele
`H2_Paternal`	Read count in H2 supporting the paternal allele
`H2_Maternal`	Read count in H2 supporting the maternal allele