User:Brady P. Dennison/Notebook/Notebook/2015/09/24

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Galaxy Bioinformatics on RNAseq


  1. Make an Account
  2. Created a History: "Pc-TF Project"
  3. Uploaded Files:
    U2OS ctrl:U2OSplus_CTTGTA.fastq.gz
    U2OS transient PcTF: U2OSneg_GTGAAA.fastq.gz
    Note: These are not the ones assigned to me, I wasn't able to use the others due to them being too large. Daniel worked on the other ones while I completed these.
  4. Set Reference as Human Feb. 2009 (GRCh37/hg19) (hg19)
  5. Ran alignment using default settings and Human (Homo sapiens) (b37): hg19 as reference genome.
  6. Took approximately 2.5 Hours, uploaded the "accepted hits" topcoat file to the server.
  7. Imported hg19_genes.gtf into my library.
  8. Used the RNA-Seq->Cufflinks option.
  9. This took about 3 hours to complete.
  10. Downloaded the "Gene Expression File".
  11. Uploaded it the the Haynes Lab server.