Pipeline was used to preprocess data for MEX — Codebook Motif Explorer & Motif Benchmarking.
The resulting data was also used for the IBIS Challenge — Codebook/GRECO-BIT open challenge in Inferring Binding Specificities of human transcription factors from multiple experimental data types.
Pipeline is described in run.sh file.
It starts with a pack of chips of the same design (we had two types of chips: 1M-ME and 1M-HK).
We have two preprocessing strategies:
- SD — spatial detrending of chip artifacts
- QNZS — quantile normalization of chip probes followed by Z-score transformation
Source data folder can be provided (default: ./source_data).
Results will be stored into two folders:
- PBM_1M-HK
- PBM_1M-ME