Where is the psiDR file?
The file can be downloaded at: http://www.pseudogene.org/psidr/psiDR.v0.txt
Is H1-hesc included in the psiDR file?
The chromatin state, promoter prediction and pol2 binding regarding to pseudogenes in H1-hesc are included in the psiDR file.
Could you let me know briefly how the chromatin states in the psiDR file are determined?
The chromatin states were assessed using the Segway segmentation. Segway annotates the genome using 25 different labels representing active and repressive marks. we use two selection criteria to pinpoint pseudogenes with active chromatin states:
(1) the frequency of the TSS is three times higher than the frequency of any repressive markers;
(2) the gene body start (GS), gene body middle (GM) and gene body end (GE) frequencies are two times larger than the frequency of the repressive markers.
The selection criteria were chosen to match the segmentation behavior of the active genes.