Welcome to Flair’s documentation!

New: Flair can now be conda installed using

conda create -n flair -c conda-forge -c bioconda flair
conda activate flair

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. (2020). 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 bed_to_psl and psl_to_bed provided in flair’s /bin directory.

Contents:

• Installing Flair
• Modules
  • flair align
  • flair correct
  • flair collapse
  • flair quantify
  • flair_diffExp
  • flair diffSplice
• Additional programs
  • diff_iso_usage
  • diffsplice_fishers_exact
  • fasta_seq_lengths
  • junctions_from_sam
  • mark_intron_retention
  • mark_productivity
  • normalize_counts_matrix
  • plot_isoform_usage
  • predictProductivity
• File conversion scripts
  • bam2Bed12
  • bed_to_psl
  • psl_to_bed
  • sam_to_map
• FLAIR2 capabilities
  • Performance increases
  • Variant integration
• Other ways to run FLAIR modules
• Other environments
  • Other methods (not recommended)
• Testing flair
• Example Files
• FAQ
  • 1. Flair collapse uses too much memory, what can I do?
• Cite FLAIR

Indices and tables

• Index

• Module Index

• Search Page