track aligns query probe sequences to any target transcriptome
Input
name:type
description
pattern
meta:map
Groovy Map containing information of the forward oriented fasta generated with the probes panel sequences generated with opt flip
e.g. [ id:'breast_cancer_probe_panel_sequences' ]
fwd_oriented_fa:file
Forward oriented fasta file generated by the opt flip command
*.fa
meta2:map
Groovy Map containing the information of the genomic features and fasta files used as references
e.g. [ id:'gencode_references' ]
ref_annot_gff:file
Reference annotation in gff format
*.gff
ref_annot_fa:file
Reference annotation in fasta format
*.fa
Output
name:type
description
pattern
probes2target
meta:map
Groovy Map containing sample information
e.g. [ id:'sample1' ]
${meta.id}/probe2targets.tsv:file
TSV file containing the gene and transcript information to which each probe aligns
*.tsv
versions
versions.yml:file
File containing software versions
versions.yml
Tools
opt
GPL-3.0 license
opt is a simple program that aligns probe sequences to transcript sequences to detect potential off-target probe activity
