FLAIR (Full-Length Alternative Isoform analysis of RNA) is a tool for the correction, isoform definition, and alternative splicing analysis of noisy reads. It is a computational workflow to identify high-confidence transcripts, perform differential splicing event analysis, and differential isoform analysis.

• FLAIR GitHub page
• FLAIR Manual

References:

• A.D.Tang, C.M.Soulette, M.J.van Baren, K.Hart, E.Hrabeta-Robinson1, C.J.Wu & A.N.Brooks
  Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns
  Nature Communications volume 11, Article number: 1438 (2020)
  

• Module Name: FLAIR (see the modules page for more information)
• Unusual environment variables set
  • FLAIR_HOME  installation directory
  • FLAIR_BIN       executable directory
  • FLAIR_SRC       source code directory
  • FLAIR_DATA  sample data directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=4 --mem=4g --gres=lscratch:10
[user@cn3200 ~]$ module load FLAIR/1.6.1
[+] Loading singularity  3.8.5-1  on cn0883
[+] Loading FLAIR  1.6.1
[user@cn3200 ~]$ flair.py
usage: python flair.py  --help
modes: align, correct, collapse, quantify, diffExp, diffSplice
Multiple modules can be run when specified using numbers, e.g.:
python flair.py 1234 ...
[user@cn3200 ~]$ flair.py align -h
usage: python flair.py align -g genome.fa -r | [options]

flair-align parse options

positional arguments:
  align

optional arguments:
  -h, --help            show this help message and exit
  -o O, --output O      output file name base (default: flair.aligned)
  -t T, --threads T     minimap2 number of threads (4)
  --junction_bed JUNCTION_BED
                        annotated isoforms/junctions bed file for splice site-
                        guided minimap2 genomic alignment
  --pychopper PYCHOPPER
                        specify cdna_classifier.py here to trim reads prior to
                        aligning
  -m M, --minimap2 M    path to minimap2 if not in $PATH
  --nvrna               specify this flag to use native-RNA specific alignment
                        parameters for minimap2
  -sam SAM, --samtools SAM
                        samtools executable path if not in $PATH
  -c C, --chromsizes C  chromosome sizes tab-separated file, used for
                        converting sam to genome-browser compatible psl file
  --psl                 also output sam-converted psl
  --quality QUALITY     minimum MAPQ of read alignment to the genome (1)
  -N N                  retain at most INT secondary alignments from minimap2
                        alignment (0)
  --quiet               Suppress progress statements from being printed

required named arguments:
  -r R [R ...], --reads R [R ...]
                        FastA/FastQ files of raw reads

Either one of the following arguments is required:
  -g G, --genome G      FastA of reference genome, can be minimap2 indexed
  --mm_index MM_INDEX   minimap2 index .mmi file

[user@cn3200 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$