Tutorial 4: 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:

If you have wget, you can download the tutorial data simply by typing

wget https://raw.githubusercontent.com/rouskinlab/seismic-rna/main/src/userdocs/tutorials/multi-sample/data.tar

Otherwise, click this link to download the tutorial data: https://raw.githubusercontent.com/rouskinlab/seismic-rna/main/src/userdocs/tutorials/multi-sample/data.tar

To ensure the download is complete and not corrupted, verify that the SHA-256 checksum is 17da8b10d2f053f7549b72c8b8dc0b37f527edca712c6f3132582e62ae3d1df0 by typing this command:

shasum -a 256 data.tar

If this command prints a different checksum, then retry the download. If the problem persists, then raise an issue (see Bugs and Requests).

After downloading and verifying the data, untar the data by typing

tar xvf data.tar

and then navigate into the data directory:

cd data

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 tutorials.