Peak-call table?

Q:
I enjoyed reading your recent STARRPeaker paper. However, when I tried to download Additional file 2: Supplementary Table S1 to get the peak calls, it returned the same PDF of the figure supplement as Additional file 1. I’d be grateful if you or a colleague would send me the table or point to where I might download it.

A:
Please see the Supplementary Table 1 file. We are working with Genome Biology to get it corrected. FYI, you can also download BED format peaks (same as Suppl. table S1) from the ENCODE project website (http://bit.ly/whg-starr-seq).

STARRPeaker publication in Genome Biology — missing Supplemental Table 1

Q:
I recently read your STARRPeaker publication in Genome Biology. The STARR-seq technology is very interesting to me, and I thoroughly enjoyed your paper. In considering my own experiments, I was looking to see through the supplemental data and noticed that link for the supplemental table 1 links to a recapitulation of the PDF of the supplemental figures (S1-S13; it’s a new file but contains the same 13 supplemental figures). Thus, Supplemental Table 1 is completely missing from the Genome Biology site. Could you or one of your co-authors forward a copy of that table to me?

A:
We will contact Genome Biology to get it corrected.

Encode for cancer genomics to predict gene expression

Q:
I am just beginning start my first ever project by using the extended gene definition provided in the dataset of Encode for cancer genomics to predict gene expressions. I would be incredibly grateful if there could be an explanation about the layout of the text files. I have been unsuccessfully trying to understand how the extended gene was used to interpret the mutations and expression changes in the published article.

A:
Thanks for your interest in the research and the extended gene annotation. We are preparing BED-formatted extended gene annotation and they will be available soon on our project website (http://encodec.encodeproject.org/). We will keep you informed.