Data tables and scripts for Transcriptome variation in human tissues revealed by long-read sequencing.
- data/: Publicly available data used in this pipeline
- analysis/: Data tables organized by analysis generated throughout the pipeline (some small tables are 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