Computational protocol: Genome-wide identification of autosomal genes with allelic imbalance of chromatin state

Similar protocols

Protocol publication

[…] Transcriptome mapping of RNA-seq reads was performed with STAR version 2.3.0 [] using the 2-pass method described in Engström et al []. Read counts for individual genes were produced with HTSeq v.0.6.0 [] using the unstranded, intersection-nonempty option with Ensembl release 67 transcript definitions. Allelic skew was estimated from allelic (cas and mus) read numbers mapped to the transcript. To identify transcripts with significant allelic skew in expression, we used regions with ≥ 15 total allele-specific reads, higher than 2-fold difference between allelic expression values, and Benjamini-Hochberg FDR < 0.05. Inferred allelic expression was estimated as a fraction of composite expression level corresponding to the observed mus:cas ratio of allelic reads. […]

Pipeline specifications

Software tools STAR, HTSeq
Application RNA-seq analysis