Pipeline FAQ - YeoLab/eCLIP GitHub Wiki

Where does my RBP bind?

The pipeline produces "Input-normalized peak" files which are BED6 formatted files containing the following columns:

1. chrom
2. start
3. end
4. -log10(p-value) from a Fisher exact/Chi square test of depth-normalized IP reads vs size-matched input reads within the given region. This is only calculated for enriched (IP > input) clusters.
5. -log2(fold change) depth-normalized IP reads / size-matched input reads
6. strand

What cutoffs should I use?

Typically, you can start with filtering peak files given -log10(p-value) >= 3 and log2(fold change) >= 3. It's also very important to view these regions on a genome browser to ensure these thresholds are appropriate for your dataset!