1. Prepare dependencies
   • IsoMut needs samtools to be installed
2. Prepare input data and reference genome
   • IsoMut expects indexed BAM files and an indexed fasta file of the reference genome as its input
   • BAM files can be generated from raw sequencing data by using an alignment software which aligns short reads to an appropriate reference genome
   • The reference fasta file is used only for alignment purposes, mutations are not detected based on the differences of the samples from the reference genome
   • Indexing of the BAM files can be done with the "samtools index" command, while indexing of the reference fasta file with the "samtools faidx" command
3. Download and compile IsoMut
4. Modify paths, directories and sample names
5. Run IsoMut
6. Interpret results

The ipython notebook below demonstrates how to run IsoMut on an example dataset of 10 DT40 samples. The BAM files only contain a short, 10 MB portion of the first chromosome, thus any biological interpretation of the results is inadvisable. The notebook can be run without any changes to it for a rapid test run.

Example dataset Example ipython notebook (HTML) Example ipython notebook (IPYNB)