test data set

Here you will find a small test data set to ensure that kallisto and pizzly are working properly. The contents are:

• transcripts.fasta.gz: a gzip compressed transcriptome
• transcripts.gtf.gz : a small subset of the GTF file for Ensembl version 85 corresponding to the transcripts provided
• reads_X.fastq.gz: gzip compressed "left" and "right" reads
• Snakefile: a sample snakemake file (not required for running kallisto or pizzly)

Running snakemake will go through the following pipeline

1. Creates the index for use with kallisto
2. Runs kallisto with --fusion to identify potential fusions
3. Runs pizzly on the kallisto output to identify potential fusions
4. Creates a new index based on the transcriptome and the fusion transcripts identified by pizzly
5. Runs kallisto in normal quantification mode on the expanded index to quantify both normal transcripts and fusions.