FASTQC output

collect_fastqc_metrics.pl will run FASTQC and generate an md5 checksum for each fastq provided in fastq_config.yaml

module load perl

perl /path/to/collect_fastqc_metrics.pl \
-d /path/to/fastq_config.yaml \
-t /path/to/fastqc_tool_config.yaml \
-c slurm \
{optional: --rna, --dry-run }

Collated output:

Filename	Total Sequences	Sequences flagged as poor quality	Sequence length	%GC	md5sum
TGL01_0001_Ov_P_EX_BAVYWVDTXY_1_R1.fastq.gz	56263351	0	126	43	bcd7a0241hc15292179a8657395181c5
TGL01_0001_Ov_P_EX_BAVYWVDTXY_1_R2.fastq.gz	56263351	0	126	44	62e60cd5313999ac907f425a2f7b7353
SMP-002-T1_EX_BAVYWVDTXY_1_R1.fastq.gz	16972293	0	126	47	bxxxxxxxxx00000
SMP-002-T1_EX_BAVYWVDTXY_1_R2.fastq.gz	16972293	0	126	46	a2b3c4d5xxxxxxxxx0021c
SMP-002-T2_EX_BAVYWVDTXY_1_R1.fastq.gz	17745387	0	126	52	yyyyyyyyyy11111
SMP-002-T2_EX_BAVYWVDTXY_1_R2.fastq.gz	17745387	0	126	51	ff29dc0312c2222262dc
SMP-002-N_EX_BAVYWVDTXY_1_R1.fastq.gz	12559524	0	126	50	zd2eeef31zz22222
SMP-002-N_EX_BAVYWVDTXY_1_R2.fastq.gz	12559524	0	126	50	z97c8881se21111

In particular, ensure read length is consistent, GC content is similar (typically between 40-60%) and files are unique (no duplicated md5sums).