Checking the quality of reads

Question

[Petchimuthu]

I need to check my quality of my forward reads. I did trimmomatic as a default setting of galaxy. But it have some errors in sequence duplication level and other parameters. I need some Short RNA read also because i want to see CRISPR sequences. How can i rectify and How can i understand backround studies of these software

[GenoMax]

There are no "errors" per se if you are referring to FastQC reports. Those reports need to be taken in context of the type of experiment being done and some of the things "failing" may be a perfectly fine result (e.g. you may have large sequence dups if you are counting CRISPRseq data).

You will find a number of excellent blog posts by authors of FastQC here: https://sequencing.qcfail.com/software/fastqc/

After reading those if you have specific questions feel free to come back to this thread and ask.