Running FASTQC Interactively

Running FASTQC interactively is good for testing.

Sample terminal command to run interactive jobs:

$ ijob -c 1 -A hpc_training -p standard -v

Copying workshop files

$ pwd

$ cp /project/rivanna-training/bioinformatics-hpc .
# . means copy it in your current working directory 

# check to make sure all files transferred:
$ ls -lh  

Running FASTQC

$ module spider fastqc

$ module load fastqc/0.12.1

$ module list

$ fastqc -t 4 -o fastqc-out ./fastqc/ecoli-fastq/SRR258*fastq.*

Notes:

• You need to know the path to your FASTQ files.
• The * wildcard (*fastq) matches all FASTQ files in the folder.
• You need to specify an output directory (fastqc-out) where the results will be saved.
• -t 4 sets the number of threads (4).

FASTQC Outputs

The above command produces .html reports.