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

meta (map)

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

txt (file)

txt file recording all distribution data in python format for each
group of reads

*.{txt}

pdf (file)

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

*.{pdf}

offset (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 (file)

File containing software versions

versions.yml

Tools

ribotish
GPL v3

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