FLAIR: Full-Length Alternative Isoform analysis of RNA

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.



Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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:

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
  -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
End the interactive session:
[user@cn3200 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$