Hello,
I would like to download data from the last release of the GLASS Consortium, but we are looking for aligned reads files in bam format. We wonder if it would be possible to obtain these type of files?
I was able to download these files already: https://www.synapse.org/#!Synapse:syn26465623
Thank you very much!!!!
Created by Henry Ruiz Garcia HenryRG The long answer: the GLASS cohort is made possible, in part, by many GLASS members graciously volunteering datasets that their labs have generated. The final cohort is an aggregate of many smaller datasets. Supplementary Table 1 of the 2019 Barthel, Johson et al paper lists all contributors to the 2019 data release, for example. Patients in the 2019 data release were treated at over 30 hospitals. This creates a legal challenge: the patient was consented for the data to be generated and analyzed and was promised certain protections. Consequently, data sharing can only occur in compliance with that consent and protected by the consenting party. It means it is challenging from a legal perspective to share the raw BAM files as it would require all those institutions to sign off on every data share. This is why we are sharing higher-level summary files via synapse.org/glass.
Tl;dr: I have added a file to the files tab that lists the accession IDs of a some of the datasets included in the cohort. Raw data (BAMs) can be obtained by applying for access to each of those.