Troubleshooting

Core Dump

If you get a Aborted (core dumped) error in the perform_kallisto_quantification step, it is likely that kallisto was not able to align any reads. This could be because of a problem with your .fastq files (e.g. they did not demultiplex correctly), you could be using the wrong reference transcriptome, or you might be using a reference transcriptome index length (given by the cycle_number parameter in the Setup section) that is larger than your read length.