HI i'm working with fastx to get the reverse_complement from fastq file downloaded from sra and separated by sra-toolkit. My problem is after using fastx reverse_complement , the overepresented sequences identified by fastqc change. I would expect the number of reads overrepresented in the two file were the same and the sequence in the second file were the reverse_complement. The command used was: fastx_reverse_complement -Q 33 -i FILE2.fastq -o FILE2_rev_com.fastq
First two examples of overrepresented sequence in original file detected by fastqc:
First two examples of overrepresented sequences in after reverse_complement over original file:
any idea what is happening here or what i'm doing wrong.