I am working on wheat genome, I want to do analyze comparative genome analysis of 3 varieties of wheat .I have sequence files from illumina 1.9 in fastq format. I checked the quality of reads by fastqc tool.GC content are not in normal range.(47- 49). What is the normal value of % GC for RNA seq reads ? The other question is that kmers are also not in correct range.How can I correct it. For trimming,adaptor seq file is required,but i don't have this file..Is that possible to remove these two error?If yes then how can I do?Can I skip the trimming step and go to next step of mapping?
In this file all parameter values are correct except kmer s and GC content.Is there any need to trim it?If yes then how can I do?