Welcome to Flair’s documentation!

FLAIR can be run optionally with short-read data to help increase splice site accuracy of the long read splice junctions. FLAIR uses multiple alignment steps and splice site filters to increase confidence in the set of isoforms defined from noisy data. FLAIR was designed to be able to sense subtle splicing changes in nanopore data from Tang et al. (2018). Please read for more description of the methods.

It is recommended to combine all samples together prior to running flair-collapse for isoform assembly by concatenating corrected read psl or bed files together. Following the creation of an isoform reference from flair-collapse, consequent steps will assign reads from each sample individually to isoforms of the combined assembly for downstream analyses.

It is also good to note that bed12 and psl can be converted using kentUtils bedToPsl or pslToBed, or using bin/bed_to_psl.py and bin/psl_to_bed.py.

Contents:

• Requirements
• FLAIR modules
  • flair align
  • flair correct
  • flair collapse
  • flair quantify
  • flair diffExp
  • flair diffSplice
• Scripts
  • predictProductivity.py
  • mark_intron_retention.py
  • diff_iso_usage.py
  • plot_isoform_usage.py
  • diffsplice_fishers_exact.py
• Other ways to run FLAIR modules
• Other environments
  • Docker
  • Conda Environment
• Example Files
• Cite FLAIR

Indices and tables

• Index

• Module Index

• Search Page