▲ 2 r/bioinformatics
ATAC seq -- data quality issue ?
Hi everyone, I am running an ATAC seq analysis. Here I largely follow the ENCODE pipeline. My input data has great quality with FastQC ≥95% >Q35. However, I realised that I was not able to generate a satisfying peak set, i.e. FRiP 6%, TSE 1.4, ca 300 peaks after idr.
Tracing back the error, I realised that after alignment with bowtie2 my read length distribution does not show the nucleosome bumps. Starting to doubt this step, I downloaded a sample from ENCODE for reference (ENCSR019XCN) and ran the exact pipeline on it, leading to the result you see here.
Now I am starting to wonder if my input data is somehow corrupt? Did the experiment fail? What could be going on here? Is there a way to salvage this?
u/bauchibaer — 11 hours ago