nf-core/slamseq

SLAMSeq processing and analysis pipeline

differential-expressionquantseqslamseqtranscriptomics

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

Launch version 1.0.0 https://github.com/nf-core/slamseq

Version history

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1.0.0 “Cobra Tin Beetle” - 2020-05-14

Initial release of nf-core/slamseq featuring:

FastQC read quality control
(Optional) Adapter trimming
Alignment filtering and multimapper recovery
SNP calling to filter T>C SNPs
Total and converted read quantification
Collapsing quantifications on gene level
Calculating QC stats
Summarising Slamdunk results
Determine direct transcriptional targets
Present QC for raw read, trimming, alignment, filtering and quantification