3 items tagged with 'kallisto'.
Pipeline for processing 10x Genomics single cell rnaseq data
Type: Nextflow
Creators: Peter J Bailey, Bailey PJ, Alexander Peltzer, Botvinnik O, Olga Botvinnik, Marques de Almeida F, Peltzer A, Sturm G
Submitter: WorkflowHub Bot
Work-in-progress
Workflow for Spliced RNAseq data Steps:
- workflow_quality.cwl:
- FastQC (Read Quality Control)
- fastp (Read Trimming)
- STAR (Read mapping)
- featurecounts (transcript read counts)
- kallisto (transcript [pseudo]counts)
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Work-in-progress
Workflow for NonSpliced RNAseq data with multiple aligners.
Steps:
- workflow_quality.cwl:
- FastQC (control)
- fastp (trimming)
- bowtie2 (read mapping)
- sam_to_sorted-bam
- featurecounts (transcript read counts)
- kallisto (transcript [pseudo]counts)
