Runs PEKA CLIP peak k-mer analysis
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
peaks:file
BED file of peak regions
*.{bed,bed.gz}
crosslinks:file
BED file of crosslinks
fasta:file
Genome reference sequence used
*.{fa,fasta}
fai:file
FAI file corresponding to the reference sequence
*.{fai}
gtf:file
A segmented GTF used to annotate peaks
*.{gtf}
cluster
meta:file
TSV file of summed occurrence distributions of k-mers within defined clusters
*.tsv
*mer_cluster_distribution*:file
distribution
TSV file with calculated PEKA score and occurrence distribution for all possible k-mers
*mer_distribution*:file
rtxn
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
*rtxn*:file
rtxn file
*rtxn*
pdf
PDF file with graphs showing k-mer occurrence distributions around thresholded crosslink sites
*.pdf
*.pdf:file
tsites
*thresholded_sites*.bed.gz:file
BED file of thresholded sites
*thresholded_sites*.bed.gz
oxn
*oxn*.bed.gz:file
BED file of oxn sites
*oxn*.bed.gz
clust
*_clusters.csv:file
CSV file of clusters
*_clusters.csv
versions
versions.yml:file
File containing software versions
versions.yml
Positionally-enriched k-mer analysis (PEKA) is a software package for identifying enriched protein-RNA binding motifs from CLIP datasets
