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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