Other ways to run FLAIR modules

For convenience, multiple FLAIR modules can be run in the same command. In place of a single module name, multiple module numbers can be specified (module numbers: align=1, correct=2, collapse=3, collapse-range=3.5, quantify=4, diffExp=5, diffSplice=6). All arguments for the modules that will be run must be provided. For example, to run the align, correct, and collapse modules, the command might look like:

flair 123 -r reads.fa -g genome.fa -f annotation.gtf -o flair.output --temp_dir temp_flair [optional arguments]

A beta version of the collapse module, called collapse-range, has been developed. The corrected reads are divided into many independent regions, which are then subject to isoform calling separately and parallelized over the number of threads specified. This dramatically decreases the memory footprint of intermediate files and increases the speed in which the module runs without altering the final isoforms. This version can be invoked by specifying collapse-range as the module (or 3.5 if using numbers). An additional program, bedPartition, needs to be in your $PATH.

flair collapse-range -r reads.bam -q query.bed -g genome.fa -f annotation.gtf -o flair.output --temp_dir temp_flair [optional arguments]

If you would prefer not to use python’s multiprocessing module, a bash script has also been provided (run_flair_collapse_ranges.sh) that runs collapse-range for the user that parallelizes using GNU parallel, which you can alter as they see fit for their system.