Setup

Before runnung MicroExonator there are several files that needs to be created inside MicroExonator/ root folder:

RNA-seq samples

Input RNA-seq data either a local_samples.tsv, NCBI_accession_list.txt or sample_url.tsv needs to be defined. If you want to run MicroExonator over RNA-seq samples that are locally stored, they need to be defined inside local_samples.tsv. MicroExonator can also download and run samples from NCBI if the corresponding SRA accession names are defined inside of NCBI_accession_list.txt, in addition any fastq.gz that can be directly download from a URL can be included into the aalysis by defining them inside a sample_url.tsv. You can find examples of these files inside the Examples/ folder. Is posible to combine different types of input sources, but at least one of these files needs to be defined inside MicroExonator/ root folder.

Cluster configuration

If you are working on a high performace cluster, then it is very likely that you need to submit jobs to queueing systems such as lsf, qsub, SLURM, etc. To make MicroExonator work with these queueing systems, you need to create a cluster.json file. We currently provide in the Examples folder a cluster.json file to run MicroExonator with lsf. To adapt MicroExonator to other quequing systems please see the SnakeMake documentation.

Config file

Each MicroExonator’s module has certain compulsory and optional parameters that needs to be defined inside a config.yaml file. The necesary content of config.yaml is described on each moudle section and examples can be found at the Examples/ folder.