gannet/Atumefaciens/20220706-snam-fastqc-fastp-multiqc-rnaseq-PRJNA316738


## QC and trimming of RNAseq data from NCBI BioProject PRJNA316738

- input_fastq_checksums.md5: MD5 checksums for original FastQs.

- multiqc_config.yaml: MultiQC config file to enable plugins (i.e. for handling fastp report processing)

- multiqc_data/: MultiQC working directory generated by MultiQC.

- multiqc_report.html: MultiQC HTML summary report.

- program_options.log: Text file documenting program options for all programs run during this Mox session.

- slurm-2779752.out: Text file generated by Mox job capturing all text printed to screen.

- <SRA_ID>.fastq: Raw RNAseq reads downloaded from NCBI SRA.

- <SRA_ID>_fastqc.html: FastQC HTML report of raw reads.

- <SRA_ID>_fastqc.zip: FastQC of raw reads output in zip format.

- <SRA_ID>.fastq.trimmed.20220706.fq.gz: fastp trimmed FastQ files in gzip format.

- <SRA_ID>.fastq.trimmed.20220706.report.html: fastp HTML report (similar to FastQC reports) showing before/after trimming metrics.

- <SRA_ID>.fastq.trimmed.20220706.report.json: fastp JSON report; used by MultiQC to generate summary report.

- <SRA_ID>.fastq.trimmed.20220707_fastqc.html: FastQC HTML report of trimmed reads. 

- <SRA_ID>.fastq.trimmed.20220707_fastqc.zip: FastQC of trimmed reads output in zip format.

- system_path.log: Record of system $PATH during Mox runtime.

- trimmed_fastq_checksums.md5: MD5 checksums of all trimmed FastQs.