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:false ]

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

alignment

meta:map

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

${prefix}/${prefix}.${suffix}:file

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

*.{sam,bam}

trans_alignments

meta:map

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

${prefix}/${prefix}.trns.txt: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

multi_bed

meta:map

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

${prefix}/${prefix}.mult.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

single_bed

meta:map

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

${prefix}/${prefix}.sngl.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

versions

versions.yml: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

bioinf.uni-leipzig.de/Software/segemehl 10.1186/gb-2014-15-2-r34
circrna
Github user nictru
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