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 also look into **DNApi : De novo adapter prediction algorithm for small RNA sequencing data** 

link:  https://github.com/jnktsj/DNApi

de novo adapter prediction (iterative) algorithm for small RNA sequencing data. DNApi requires Python (2 or 3) under a Linux/Unix environment. DNApi accept (un)compressed FASTQ files or redirected standard input (stdin) as an input. You can simply run:

    $ python dnapi.py <fastq>

or

    > $ <process-generates-fastq> | python dnapi.py -

To see the detailed usage, type:

    $ python dnapi.py [-h | --help]

DNApi can predict most 3′ adapters correctly with the default parameters. However, if you want to tweak the parameters or want to run other prediction modes, see [prediction modes and parameters] (https://github.com/jnktsj/DNApi#prediction-modes-and-parameters) for more detail.
