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irap - integrated RNA-seq Analysis Pipeline

  •    R

iRAP is a flexible RNA-seq analysis pipeline that allows the user to select and apply their preferred combination of existing tools for mapping reads, quantifying expression and testing for differential expression. Depending upon the application, iRAP can be used to quantify expression at the gene, exon or transcript level. Please consult the wiki (https://github.com/nunofonseca/irap/wiki) for further information.

zUMIs - zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

  •    R

zUMIs is a fast and flexible pipeline to process RNA-seq data with (or without) UMIs. The input to this pipeline is simply fastq files. In the most common cases, you will have a read containing the cDNA sequence and other read(s) containing UMI and Cell Barcode information. Furthermore, you will need a STAR index for your genome and GTF annotation file.