Example 3) Running multiple samples at once

SEISMIC-RNA allows for multiple samples to be run with one simple command.

Download example files

Paired-end FASTQ files were generated using seismic sim. The files, with their corresponding reference fasta file, can be downloaded here: https://raw.githubusercontent.com/rouskinlab/seismic-rna/main/src/userdocs/examples/MultiSample/fq/MultiSample.zip

Run the SEISMIC-RNA workflow

To run multiple samples at once, all that is needed is to provide a directory where all the desired FASTQ files can be found (they can even be distributed in subdirectories without it being an issue). If the different FASTQs are to be aligned against the same reference, then a single sequence in a fasta file will suffice. If the FASTQs are to be aligned against more than one sequence, then the fasta file must contain all the desired sequences:

seismic wf fq/sim_multiple.fa -x fq/

Output

In the chosen output folder (./out by default), directories with the names of each sample will be created, each one with the same subdirectories already described in the previous examples.