Published April 27, 2021
| Version 1.0.0
Software
Open
nf-core/clipseq: nf-core/clipseq 1.0.0 - Ianthine Pelican
Creators
- 1. The Francis Crick Institute
- 2. Science for Life Laboratory
- 3. Francis Crick Institute
Description
Initial release of nf-core/clipseq, created with the nf-core template.
Pipeline summary- Adapter and quality trimming (
Cutadapt
) - Pre-mapping to e.g. rRNA and tRNA sequences (
Bowtie 2
) - Genome mapping (
STAR
) - UMI-based deduplication (
UMI-tools
) - Crosslink identification (
BEDTools
) - Bedgraph coverage track generation (
BEDTools
) - Peak calling (multiple options):
iCount
Paraclu
PureCLIP
Piranha
- Motif detection (
DREME
) - Quality control:
- Sequencing quality control (
FastQC
) - Library complexity (
Preseq
) - Regional distribution (
RSeQC
)
- Sequencing quality control (
- Overall pipeline run and QC summaries and peak calling comparisons (
MultiQC
)
Files
nf-core/clipseq-1.0.0.zip
Files
(2.3 MB)
Name | Size | Download all |
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md5:8cb1da8f87d7ea58fa0dc15edb28da77
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2.3 MB | Preview Download |
Additional details
Related works
- Is supplement to
- https://github.com/nf-core/clipseq/tree/1.0.0 (URL)