Description

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

reads (file)

FASTA or FASTQ files

*.{fa,fasta,fq,fastq,fq.gz,fastq.gz}

fasta (file)

Reference genome FASTA file used to construct Segemehl

*.{fa,fasta}

index (file)

Segemehl Index file from SEGEMEHL_INDEX

*.idx

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

alignment (file)

File containing genomic alignments in SAM format
(please add “-b” flag to task.ext.args for BAM)

*.{sam,bam}

trans_alignments (file)

Custom text file containing all single split alignments predicted to be in trans
(optional, only if -S flag is set in task.ext.args)

*.trns.txt

single_bed (file)

Bed file containing all single splice events predicted
in the split read alignments.
(optional, only if -S flag is set in task.ext.args)

*.sngl.bed

multi_bed (file)

Bed file containing all splice events predicted
in the split read alignments.
(optional, only if -S flag is set in task.ext.args)

*.mult.bed

versions (file)

File containing software versions

versions.yml

Tools

segemehl
GPL v3

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection