DASiRe

What is DASiRe?

Direct Alternative Splicing Regulator predictor (DASiRe) is a web application that allows non-expert users to perform different types of splicing analysis from RNA-seq experiments and also incorporates ChIP-seq data of a DNA-binding protein of interest to evaluate whether its presence is associated with the splicing changes detected in the RNA-seq dataset.

DASiRe is an accessible web-based platform that performs the analysis of raw RNA-seq and ChIP-seq data to study the relationship between DNA-binding proteins and alternative splicing regulation. It provides a fully integrated pipeline that takes raw reads from RNA-seq and performs extensive splicing analysis by incorporating the three current methodological approaches to study alternative splicing: isoform switching, exon and event-level. Once the initial splicing analysis is finished, DASiRe performs ChIP-seq peak enrichment in the spliced genes detected by each one of the three approaches.

Serverside

Start the serverside app by running the following command from the top directory of this git. (server-update.sh is a prerequisite for internal use only)

 docker run -v $(pwd)/serverside/R:/srv/shiny-server/ --rm --name 'dasire' -p 3838:3838 -d marisalb/dasire:server

Preprocessing

Start preprocessing pipeline by first dropping all of your inputs in MOUNT/input directory and re-write your config file.

MOUNT/
├──input/
|   ├── adapters_pe.fa
|   ├── ENCFF239POR_1.fastq
|   ├── ENCFF239POR_2.fastq
|   ├── ENCFF250AJS_1.fastq
|   ├── ENCFF250AJS_2.fastq
|   ├── ENCFF301JRH_1.fastq
|   ├── ENCFF301JRH_2.fastq
|   ├── ENCFF803NZJ_1.fastq
|   ├── ENCFF803NZJ_2.fastq                     # Also, mention these files in the config file
|   ├── gencode.v36.annotation.gff3             # gff=/MOUNT/input/gencode.v36.annotation.gff3
|   ├── gencode.v36.annotation.gtf              # gtf=/MOUNT/input/gencode.v36.annotation.gtf
|   ├── gencode.v36.transcripts.fa              # transcripts_fasta=/MOUNT/input/gencode.v36.transcripts.fa
|   ├── GRCh38.primary_assembly.genome.fa       # fasta=/MOUNT/input/GRCh38.primary_assembly.genome.fa
|   └── metadata.txt                            # metadata=/MOUNT/input/metadata.txt
└── config.sh                          <---# Hosted above the input directory.

Also add the number of cores you want DASiRe to use with nCores=4. I'd recommend 4 on a laptop with 6-8 cores.

The pipeline uses the following software versions:

• GNU parallel 20161222
• MultiQC v1.12
• Kallisto:0.48.0
• STAR: 2.7.10a
• samtools Version: 1.7 (using htslib 1.7-2)
• majiq 2.1
• genomicranges:1.46.1
• genomicfeatures:1.46.1
• genomicalignments:1.30.0
• isoformswitchanalyzer:1.16.0
• deseq2:1.34.0
• dexseq:1.40.0
• rsubread:2.8.1

To start the DASiRe pipeline, please run the following command in this git's main directory.

docker run -v $(pwd)/MOUNT:/MOUNT --user $(id -u):$(id -g) --name 'dasire-preprocessing' --rm marisalb/dasire:client