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 correct Corrects misaligned splice sites using genome annotations and/or short-read splice junctions. Based on common user issues we have encountered, for flair-correct to run properly, please ensure/note that (1) the genome annotation and genome sequences are compatible, (2) gtf is preferred over gff for annotation and annotations that do not split single exons into multiple entries are ideal.

Inputs

1. Uncorreced bed12 file.
2. FASTA file of the reference genome.
3. GTF annotation file.
4. BED format splice junctions from short-read sequencing or GTF annotation file.

Outputs

1. bed12 of corrected reads,
2. bed12 of reads that weren't able to be corrected,
3. psl of corrected reads if the -c chromsizes file is provided.

Either (1) or (3) can be supplied to flair-collapse as the query.

More Information

See the excellent FLAIR documentation

Galaxy Wrapper Development

Author: Florian Heyl