ASGAL

Warning

ASGAL requires the variables $fastqpair1suffix and $fastqpair2suffix to be set in the scripts/asevent_config.sh file.

ASGAL Factsheet

Toolname	asgal
Version	1.1.6
License	GNU General Public License version 3

Required Files

• fastq , fasta , gtf

Links

• ASGAL manual

• ASGAL publication: ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events

Parameters

These are the default parameters set in the src/asgal/ENTRYPOINT.sh script. If you want to change it you can do this in the ENTRYPOINT script directly. Please refer to the ASGAL manual.

--multi

Set multi option.

-g

Reference genome in fasta format.

-g $fasta

-a

The path to the gene annotation file in GTF format for annotation of fusion junctions.

-a $gtf

-t

Transcript file.

-t $transcript

-s

Fastq filename of paired end read 1.

-s *yourFastqFile1_*1.fastq

-s2

Fastq filename of paired end read 2.

-s2 *yourFastqFile1_*2.fastq

-o

Output directory. The output will be separated into case and control folder based on the basefolder of the according fastq file.

-o $outdir

-@

Number of threads to be used during the computation

-@ $ncores

--allevents

Report all events, not only novel ones.