I have sent to sequence my RNAseq experiment to Macrogene. They used NovaSeq (Illumina Platform) to sequence my samples. I asked for 20M reads paired-end 150 bp length. I have made the FASTQC analysis of the raw reads and some samples showed strange Kmer-content graphs with an increase of specific k-mers from position 90. The trimming (I used Trimmomatic) eliminated 15-25% of reads in those libraries. Finally, I mapped against the genome and only 50% of reads mapped. The genome sequences are fine because a colleague used them to map other RNAseq experiment and obtained 80% of mapped reads. So, I think that it was a problem during the library preparation or the sequencing process.
Here is the link to the image: https://www.dropbox.com/s/4npf8zr929mhqep/kmer_profiles.png?dl=0
Thanks for your help