Some of our FastQC reports have a module marked as “red cross” (interpreted as “very unusual”), for example, “Kmer Content”.
We need to run Tophat+Cuffdiff on those fastq data, so I am wondering whether we should not use the fastq data to run Tophat+Cuffdiff if any of its modules is marked as “red cross”?
As for “Kmer Content”, I am wondering how important this module is?
I read the online document on “Kmer Content” (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/11%20Kmer%20Content.html ), but did not seem to find its significance level.
Is the order of the modules listed the order of their significance (are the top ones more significant than the bottom ones)?
Also, I wonder what tools may be used to fix the problems reported by FastQC?
Any ideas and advice would be greatly appreciated!
Thank you very much!