What it does

FLAIR FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads. 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). 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.

flair collapse Defines high-confidence isoforms from corrected reads.

Inputs

1. Corrected Reads as Bed12 File.
2. FASTA/FASTQ file of raw reads. All raw read fastq/fasta files should be concatenated into a single file.
3. FASTA of Reference Genome.
4. GTF annotation file.
5. Promoter regions bed file to identify full-length reads.

Outputs

Outputs the high-confidence isoforms in several formats: (1) bed, (2) gtf, (3) FASTA.

More Information

See the excellent FLAIR documentation

Galaxy Wrapper Development

Author: Florian Heyl