I have done
fastqc on paired end fastq files for RNA. I have got an error for duplicate reads as most of the files failed for this criteria. I want filter duplicate reads in these fastq files and blast them to see what they actually are. I have seen some posts discussing about duplicate reads but I am looking for a way to filter out the duplicate reads from fastq files.
I have got another warning for some of the overrepresented sequences. Is there a way to deal with such sequences? There was no error for adapters but I am still removing the adapter sequences as I ran fastqc before doing that. thank you for the help!