I am analysing the ROSMAP RNA-Seq data and I was wondering whether I can download the batches for each sample along with the plate used.
Also, how were batch effects controlled for during the data processing? And what about the first 12 "deep coverage" references?
Created by Javier Simón-Sánchez simonsanchezj @simonsanchezj - we just noticed that the 2 files with specimen ID '150_120419_0' are duplicates. We believe the missing deep coverage sample is '492_120515', but need to verify this. Will give you an update Specifically, the those 12 files are these:
${synapsetable?query=SELECT id%2Cname%2CspecimenID%2Cassay%2CdataType FROM syn11346063 WHERE %28 %28 "study" %3D %27ROSMAP%27 %29 AND %28 "assay" %3D %27rnaSeq%27 %29 AND %28 "fileFormat" %3D %27bam%27 %29 %29 AND specimenID like %27%25%5F0%27&showquery=true} Hi Javier, the batch information can be found in this file: syn4300313. Batch 0 are the 12 samples with deep coverage.