Description

flip corrects probes that are aligning to the opposite strand of their intended target genes by reverse complementing them

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information of the probe panel sequences used for the xenium experiment e.g. [ id:'breast_cancer_probe_panel_sequences' ]

probes_fasta:file

Fasta file for the probe sequences used in the xenium experiment

*.fasta

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 annotations in gff format

*.gff

ref_annot_fa:file

Reference annotations in fasta format

*.fa

Output

name:type
description
pattern

fwd_oriented_fa

meta:map

Groovy Map containing information of the forward oriented fasta generated with the probes panel sequences ‘opt flip’ e.g. [ id:'breast_cancer_probe_panel_sequences' ]

${meta.id}/fwd_oriented.fa:file

The forward oriented fasta file

*.fa

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

github.com/JEFworks-Lab/off-target-probe-tracker github.com/JEFworks-Lab/off-target-probe-tracker/blob/main/README.md https://github.com/JEFworks-Lab/off-target-probe-tracker
included in
spatialxe
maintainer
Github user khersameesh24
get in touch
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