Splicing tools

Warning

Currently only alternative splicing event detection is supported. Differential splicing tools are coming soon. The differential splicing function of tools which are able to compute both alternative and differential splicing the differential mode is still in beta.

For splicing tools we differentiate between alternative and differential splicing tools. Some tools are able to compute both. Differential splicing tools compute alternative splicing for two conditions (e.g. case and control) and the files should be separated as indicated by our input directory structure. For alternative splicing analysis “control” is the default.

Splicing Input Files

Tip

The paths assume you are using our suggested input structure. Example input files you can find in our examples section.

You can find the required input files in the tool-specific documentation.

fastq

Fastq files for pair 1 and 2 fastq files stored in $fastqdir, identified by the suffix $fastqpair1suffix and $fastqpair2suffix respectively. Not all splicing tools work with fastq files. The path variables can be found in scripts/config.sh and scripts/asevent_config.sh. For differential splicing the files need to be separated in controldir and casedir

# Fastq file paths
# Assumed variable settings:
#    $fastqdir=input/fastq   ## in config.sh
#    $fastqpair1suffix="_1.fastq"   ## in asevent_config.sh
#    $fastqpair2suffix="_2.fastq"   ## in asevent_config.sh
# Replace the text between the stars *...* with your file names

input/controldir/fastq/*yourFastqFile1*_1.fastq
input/controldir/fastq/*yourFastqFile1*_2.fastq
input/controldir/fastq/*yourFastqFile2*_1.fastq
input/controldir/fastq/*yourFastqFile2*_2.fastq
. . .

bam

Bam files created by a mapping tool of your choice. When DICAST is run as a pipeline, these will be created by the selected mapping tool(s).

input/controldir/fastq/*yourFastqFile1*_1.fastq

fasta:

The name of the reference fasta file. The path variable can be found in scripts/config.sh.

# Fasta files paths
# Replace the text between the stars *...* with your file name

input/*yourFastaFile*.fa

transcript

The name of the fasta file for gene transcripts. The path variable can be found in scripts/asevent_config.sh.

# Assumed variable settings:
#    $inputdir=input   ## in config.sh

input/*yourTranscriptFasta*.fasta

gtf

Gene annotation file in GTF format.

# Replace the text between the stars *...* with your file name

input/*yourGTFfile*.gtf

gff

Gene annotation file in GFF format.

# Replace the text between the stars *...* with your file name

input/*yourGFFfile*.gff

Parameters

To provide a fair baseline while maintaining easy usability, per default we run the tools with their default variables. The default parameters can be changed by editing the ENTRYPOINT.sh scripts of each tool. The variables used by mapping ENTRYPOINT.sh scripts can be set in the config.sh and asevent_config.sh files in the scripts folder. For a usual analysis you should not need to change these parameters.