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
You can use [fastp](https://github.com/OpenGene/fastp) to trim adapters for Illumina sequencing data, without the need of knowing the adapter sequences.   

Just download fastp and run:

    fastp -i in.fq -o out.fq

And then everything is done, the adapters are trimmed in out.fq   

For paired end data, the command is like:

    fastp -i in1.fq -o out1.fq -I in2.fq -O out2.fq

Gzip is supported for both input and output.