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?


file:///home/comsats-ra/fatimamphilldata/G1_cleaned_R1_fastqc.html#M11
One expects many failed FastQC modules in RNAseq datasets. GC content should be similar over samples, but otherwise ignore a "Fail" in FastQC there. Similarly, you expect enriched k-mers. You should not attempt to correct this, it's already correct.

You can trim reads with `Trim Galore!`, which has the default adapters all built in. Having said that, it's quicker to just use STAR for alignment, in which case you don't need to bother trimming adapters.