RNASeq RSEM Pipeline

This pipeline runs RSEM for given libraries. Please use the clip below for running the pipeline. If you have any questions or need modifications in the pipeline please send an email to biocore@umassmed.edu.

      This pipeline running the steps below;
      1. stepRibo: Ribosomal RNA mapping
      2. stepRSEM: mapping and RSEM quantification
      3. stepIGVTDF: This creates tdf files for IGV visualization
      4. stepRSEMCount: It creates a table that includes TPM values for each gene
      5. stepRSEMRawCount: It creates a table that includes ExpectedCounts for each gene. (Since, we use this file in DESeq analysis)
      6. stepBam2BW: It creates BigWig files for UCSC genome browser visualization