Episode III.5: Rogue Isoforms
Takes R2C2/C3POa data and defines high confidence isoforms.
This repository for Mandalorion is feature frozen. The most up to date version of Mandalorion can be found here.
The paths to these will need to be put into your config file like this. If you have the program installed or in your path already, replace the path with the name of the program.
python3 Mandalorion.py [OPTIONS]Running with default settings:
python3 Mandalorion.py -c config_file -p . -g gencodeV29.gtf -G hg38.fasta -a adapters.fasta -f R2C2_consensi.fasta -b R2C2_subreads.fastqRequired options:
-c config file containing paths to required dependencies (above)
-p output path
-g annotation file (gtf)
-G genome file (fasta)
-a adapter file (fasta)
-f R2C2 read file (fasta, can be comma separated list)
-b R2C2 subread file (fastq, can be comma separated list)
Tweakable parameters:
-u upstream buffer, defines leniency window for TSS and polyA definition (default 10)
-d downstream buffer, defines leniency window for TSS and polyA definition (default 50)
-s subsample consensus, defines how many random subreads are used to make isoforms (default 500)
-r minimum ratio, proportion of reads that align to a locus required for an isoform (default 0.01)
-i minimum internal ratio (default 1)
-R minimum number of reads for an isoform (default 5)
-O overhangs, defines bounds for unaligned bases on ends, format: min5',max5',min3',max3' (default 0,40,0,40)
-t number of threads to use for minimap2 (default 4)
-e ends, the ends of your sequences, format: 5prime,3prime (default 'ATGGG,AAAAA')
-I minimum isoform length (default 500)
-n minimum feature count (number of reads, default 2)
-w splice site window (default 1)
-A A proportion cutoff - isoforms with A content within a 30 nt window around the polyA higher than this will be discarded (default 0.5)
These are the scripts used in the paper to do haplotype phasing and HLA analysis.