To get a FastQC report for your FASTQ files, run the public FastQC analysis workflow. FastQC is a graphical software so if you use it in Puhti you will need a working X-term connection (FreeNX. Select the Example Form on the Revisions tab In order to do fixed trimming with the fastq file bad_example. Quality control using FASTQC, This could work: find -maxdepth 5 -name '*fastq. This would allow FastQC to be run as part of an analysis pipeline. fasta file and will write the desired output file, workshop_example. reads from Illumina or PacBio sequencing). The FastQC software is a popular way to evaluate the quality of high-throughput sequencing reads (e.
Input to FastQC is a sequencing file in (compressed) fastQ format containing reads and quality information. fastq exit 0 Substitute all variables that you would like to change from the parameter file with a variable notation, in the form of $1, $2, $3, etc for the first, second, third, etc input parameter. You can copy and paste the token into the R console, press enter, and then the function will save the token as an character object token in the current workspace, which will make it convenient for you to use it in the next steps.
