How can i identified the linkers in ChIA-PET fastq file? I read something that it says that it in the right end of the sequence. But when i search in Encode protocols about experiment procedures, i did not find informations about linker sequences. I realized that many places the linker sequences lA "GTTGGATAAG" and linker B:GTTGGAATGT and some bioinformatics tools ,like Mango, use its as default by linker filtering . But i still don't understand how i can reconized the linker in a fastq sequence or other way that i can find this information, because i see other linker sequences and thus this is not the same for all ChIA-PET experiments.
Thanks in advance.