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PostPosted: Tue Oct 05, 2021 10:45 am
by cpere117
In this forum, I will be discussing the steps I took in order to complete the RNA-Seq analysis for dbGap PAH dataset phs000998.v2.p1. In this dataset we have induced pluripotent stem cells derived from PAH patients at the Stanford medical center. We had protected access to this data so we had to use the SRAToolkit to derive the fastq files.The first post I will make will be regarding the demographics of this dataset. Next, I will show the results of quality control analysis of these data samples using (fastqc and trimmomatic). Following this, I will then do alignment with HISAT here at path4 and annotate using tophat. Differential Gene Expression analysis will then be conducted using either Limma or EdgeR. Finally, I will discuss the process of selecting gene candidates related to significant ID3 or NRF1 targets. Thank you.