lorals_paper_code

Data tables and scripts for Transcriptome variation in human tissues revealed by long-read sequencing.

Overview of repository

• data/: Publicly available data used in this pipeline
• analysis/: Data tables organized by analysis generated throughout the pipeline (some small tables are included)

Analyses included

• Qualitative control:
• Qualitative control by NanoPlot
• Three prime bias using the mitochondrial transcripts
• Overview of the dataset aligned to GENCODEv26
• Call new transcript with flair:
• Flair and TransDecoder pipeline to call novel transcripts
• Comparison of FLAIR novel transcripts to other datasets
• Overview of the dataset aligned to FLAIR
• Differential transcripts across tissues:
• Differential transcript expression and usage across tissues
• Allelic analysis:
• Analysis of allelic counts from genes and transcripts
• Comparison to GTEx eQTLs and sQTLs
• Stratification by alternative transcript structure event
• Analysis of enloc
• PTBP1 knockdown:
• Allele analysis in fibroblast cell lines with PTBP1 KD
• Comparison to ENCODE eCLIP sites
• Variant interpretation and rare variant analysis:
• Variant annotation using new flair transcripts
• Rare variant interpretation using new flair transcripts