Here is a link to the following dataset:
https://figshare.com/articles/BAM_and_BAI_files/4530707/1

Data posted by: Reetta Holmila: Massively parallel deep sequencing of plasma cfDNA methylation in HCC and controls (categories: biomarkers)

This page lists both the BAM and BAI files.

Quick followup:

Is this DNA-Seq data or bisulfite sequencing data?

I looked over the data information, and it does appear to be bisulfite sequencing data. I found this paragraph detailing the data:

"Massively parallel deep bisulfite sequencing of plasma cfDNA methylation in HCC
Published on 09 Jan 2017 - 00:14 by Reetta Holmila
In this study, we applied targeted massively parallel semiconductor sequencing to assess methylation on a panel of genes (FBLN1, HINT2, LAMC1, LTBP1, LTBP2, PSMA2, PSMA7, PXDN, TGFB1, UBE2L3, VIM and YWHAZ) in plasma circulating cell-free DNA (cfDNA) and to evaluate the potential of these genes as HCC biomarkers in two different series, one from France (42 HCC cases and 42 controls) and one from Thailand (42 HCC cases, 26 chronic liver disease cases and 42 controls). We also analyzed a set of HCC and adjacent tissues and liver cell lines to further compare with ‘The Cancer Genome Atlas’ (TCGA) data."

Link to that page: https://figshare.com/projects/Massively_parallel_deep_bisulfite_sequencing_of_plasma_cfDNA_methylation_in_HCC/18185

Also need to locate BAM files from sequencing of non-bisulfite converted samples from individuals with structural variations.

Un-assigning as Ahn is moving on to her next rotation. Good luck with everything!

Data sets from genome sequencing saved in IGB Dropbox under "Jira issues" folder for this issue.
Data are from twitter thread w/ Brent Pedersen from Aaron Quinlan lab University of Utah. See attached.
Marking this as closed (for now) as we now have a good handle on how to get more data & where to find potential reviewers/representative users:

• Brent Pedersen, Quinlan lab (working on structural variants)
• Greenwood Genetics (human genetics clinic in South Carolina)
• Canadian Bioinformatics workshop on genomic medicine instructors & attendees (attended by Nowlan & Ann, 2018)
• Wake Forest human genetics and genomics faculty
• Steve Chervitz Trutane (Personalis)
• Clinical variant analysts (https://www.linkedin.com/in/shelly-sorrells-phd-2a46333b/)