nf-core/cageseq

CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.

cagecage-seqcageseq-datagene-expressionrna

This pipeline uses DSL1. It will not work with Nextflow versions after 22.10.6. Learn more.

Launch version 1.0.2 https://github.com/nf-core/cageseq

Version history

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Fixed

reads the —input parameters correclty
cleaned up multiqc config

Added

Update template to nf-core/tools 1.12.1

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`Fixed`

clusters on the negative strand were not included in the final output file
bigwig export needs sorted input

`Added`

Update template to nf-core/tools 1.12

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v1.0.0 (Gold Lion) - [2020-10-16]

Initial release of nf-core/cageseq, created with the nf-core template.

Pipeline summary

Input read QC (FastQC)
Adapter + EcoP15 + 5’G trimming (cutadapt)
(optional) rRNA filtering (SortMeRNA),
Trimmed and filtered read QC (FastQC)
Read alignment to a reference genome (STAR or bowtie1)
CAGE tag counting and clustering (paraclu)
CAGE tag clustering QC (RSeQC)
Present QC and visualisation for raw read, alignment and clustering results (MultiQC)