This Perl script runs FastQC program on input FASTA files, detects the overrepresented sequences from FastQC report and trims the sequences using cutadapt tool. FastQC is run again on the trimmed fastq files for comparison.
Download the fastqc_cutadpt folder and run as described below.
perl fqstqcCutadapt.pl -1 <R1.fastq.gz> -2 <R2.fastq.gz>| Argument | Description |
|---|---|
-1 |
R1 FASTQ file |
-2 |
R2 FASTQ file |
--nofastqc |
[FLAG] First round of FastQC is skipped and FastQC result is read directly from --fastqcOut option. Default: FastQC is run. |
--adapters |
[STR] FASTA file with Illumina adapters. Default: data/universal_adapters.fasta |
--fastqcOut |
[STR] Directory to store the FastQc result. Default: fastqc |
--trimmedOut |
[STR] Path to store trimmed FASTQ files. Default: fastq_trimmed |
--help |
Show this scripts help information |
MIT