Description

Quality control of riboseq bam data

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

bam:file

Sorted BAM/CRAM/SAM file

*.{bam}

bai:file

Index for sorted BAM/CRAM/SAM file

*.{bai}

meta2:map

Groovy Map containing reference information e.g. [ id:'Ensembl human v.111' ]

gtf:file

GTF-format annotation file for reference sequences used in the bam file

*.gtf

Output

name:type
description
pattern

distribution

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.txt:file

file containing distribution

*.{txt}

pdf

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.pdf:file

Pdf figure file is plot of all the distributions and illustration of quality and P-site offset

*.{pdf}

offset

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.para.py:file

This file saves P-site offsets for different reads lengths in python code dict format, and can be used in further analysis

*.{para.py}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

ribotish
GPL v3

Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data.