I am working through the Galaxy training tutorial to analyse CLIPseq data on the Galaxy / CLIP-explorer server. (CLIP-Seq data analysis from pre-processing to motif detection)
I was wondering if someone knows why the Peak caller ( PEAKachu) does not call the peak (Chr17 8,364 Mb - 8,370 Mb region) that was published in the paper on which the training set is based on. The fold enrichment was reported to be >8 for this which is well above the threshold set in the peak caller.
I also analyzed one complete replicate (REP2) from yeolab (original data) and the Peak caller still did not return the expected RBFOX2 peak)