Alternative splicing tools parameters

Found in file: scripts/asevent_config.sh

This config file sets parameters that are specific to AS event detection tools only.

Basic Parameters

transcript

Fasta file for gene transcripts.

Default: $fasta (set in config.sh, see the General Parameters)

star_alignment_files

Path to the folder containing star alignment files (*.SJ.)

Default: $workdir/output/star-output

Note

We support only paired RNA-Seq - fastq files have to be in pairs.

Set the suffixes parameters (including the file extension) for all fastq pairs (e.g. _1.fastq and _2.fastq).

fastqpair1suffix

Suffix for the first file of the fastq pair.

Example: _1.fastq

fastqpair2suffix

Suffix for the second file of the fastq pair.

Example: _2.fastq

use_bam_input_files

Determines what kind of input to use: 1 for bam files, 0 for fastq files.

Default: 0

combine_events

Events such as Multiple Exon Skipping should be represented as such, instead of individual exon skipping events.

Default: 1

Warning

Something broke while changing the config file? Make sure there is no space between the variable, the equal sign and the value.

Since these files are bash scripts, it is important to mind the syntax rules. E.g., there can’t be a whitespace before and after “=”.

For example: | Wrong: workdir = “dockers/” | Right: workdir=”dockers/”