I analysing some RNA-seq samples from cancer patients with default parameters in tophat. My reads are paired end reads, and the right reads mapping percentage and control quality is good.
However, the mapping rate of the left reads is around 50%, and I have high enrichment of k-mers in the middle of this reads, across all the samples of the experiments. The rest of the QC looks good for the samples.
I am afraid that I am getting low mapping rates because of this. What should I do? or how should I remove them as they are in the middle of the reads
I am attaching some figures of the kmer content.