I am trying to identify the adapter sequences of my ATAC-sequencing data. The way I tried to achieve this was to send the fastq file to FastQC. Hoping the sequence would be picked and showed in the report.
In the report, there was no overrepresented sequences shown in the overrepresented sequences section, but in adapter content graph, it indicated the reads contain Nextera Transposase Sequence. That's what confused me as I expected the adapter sequence (Nextera Transposase Sequence) would be picked up in overrepresented sequences section? or am i wrong?
I looked around in internet and found the Nextera Transposase Adapters from illumina document:
Read 1 5’ TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG Read 2 5’ GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
Does anyone know if the above sequences are the corrected adapter sequence ? Thanks