dear?from paper I have known the eQTL analysis need RNA-seq processed expression data and imputed genotype data.
I would like to ask if there is any ROSMAP RNA-seq processed expression data?
I noticed there are some ROSMAP RNAseq Picard metrics data (https://www.synapse.org/#!Synapse:syn3388564)? Are these the data I want to get?
If so, What is the difference between ROSMAP_RNAseq_FPKM_gene.tsv and ROSMAP_RNAseq_FPKM_isoform.tsv?
Another question is which software you choosed to make eQTL analysis?
I'm looking foward to hearing from you soon.Thank you very much!
Created by xiaoyan li adelalady Information about ROSMAP RNAseq can be found at syn3388564.
The Picard metrics are for quality control purposes, but the two files you mentioned are likely what is necessary - Maybe @sieberts or @th_vairam can comment further, thanks.
I believe that 'isoform' versus 'gene' files differ in how the expression level was quantified - summed for individual isoforms of the same gene ('isoform') or all overlapping isoforms of a gene together ('gene'). RSEM was used, so you might check the documentation for that program (https://github.com/deweylab/RSEM).