Pipeline for high-confidence allele-specific analysis of RNA-seq at scale.

This R-package performs sample overdispersion estimation from RNA spike-ins or technical replication.

Citation: A. Mendelevich, S. Gupta, A. Pakharev, A. Teodosiadis, A. A. Mironov, A. A. Gimelbrant. Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale. Bioinformatics 39, i431–i439 (2023). link

docker pull sasha/ase

or

remotes::install_github("gimelbrantlab/controlFreq")

compute_iQCC_for_selected_samples(df = allelic-counts-table, reps = 1:10, sup_Q = 30)

see Wiki for more details.

• For allelic bias test and differential AI test, see Qllelic R-package functions and "Replicate sequencing libraries are important for quantification of allelic imbalance", A.Mendelevich et.al.

• For data preprocessing procedure used in the paper and relevant recommendations, see fastq2allelictabs repository.

Figure above was made in biorender.