Hello,
Could you please help to understand the ROSMAP data available in the RNA-seq Harmonization Study? Specifically I am interested in the re-processed STAR aligned bam files here: https://www.synapse.org/#!Synapse:syn8540863
It appears that for ROSMAP there are 639 bam files put on synapse from this re-processing effort, even though it is said to be done on 1168 total samples from all the brain regions. Do you know why this is?
Thank you.
Created by Grace Xiao gracexiao99 Hi there, the aligned bam files you linked above are from the original RNAseq reprocessing study done several years ago, which used the GRCh37 build. The updated version using GRCh38 is [here](https://www.synapse.org/#!Synapse:syn21241740). For the updated version, there are 1168 ROSMAP samples included, but we do not have the aligned bam files. We have the STAR alignment metrics and gene counts for each batch, as well as provenance files indicated all of the unaligned bams used as input for the alignments and gene quantifications for each cohort/batch.
[This link](https://adknowledgeportal.synapse.org/Explore/Data?QueryWrapper0=%7B%22sql%22%3A%22SELECT%20*%20FROM%20syn11346063.24%22%2C%22limit%22%3A25%2C%22offset%22%3A0%2C%22selectedFacets%22%3A%5B%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22study%22%2C%22facetValues%22%3A%5B%22RNAseq_Harmonization%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22resourceType%22%2C%22facetValues%22%3A%5B%22experimentalData%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22fileFormat%22%2C%22facetValues%22%3A%5B%22csv%22%5D%7D%5D%2C%22sort%22%3A%5B%7B%22column%22%3A%22name%22%2C%22direction%22%3A%22DESC%22%7D%5D%7D) is a portal query of all the "provenance.csv" files in this study, which contain the synIDs of all input bam files used for each alignment, if you are interested in downloading the original unaligned bam files used in the harmonization pipeline.