So, I have ChIP-seq sample with this barcode: CGATGT and I want to remove the barcodes and adapters. But when looking to fastqc files in the headers has 'CTTGTA'
@NS500672:149:HNNH3BGXY:4:23612:26287:20351 1:N:0:CTTGTA TCCGTCTAGTCAAAGCTATGGTTTTTCCAGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCCTAT TATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATATCGTATGCCGTCGTCTGCGTGAAAAAAAAAAGCGGGGG
a) Shouldn't it be CGATGT, as the barcode?
Also, when running fastqc there are overepresented sequences and it says possible source TrueSeq adapter, Index 12, which has the CTTGTA barcode, as shown in page 22 in here: https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences-1000000002694-05.pdf
The adapter content on FastQC is ok.
b) What does this mean?
I am new to chip-seq..