Galaxy Bioinformatics on RNAseq
Steps:
- Make an Account
- Created a History: "Pc-TF Project"
- 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.
- Set Reference as Human Feb. 2009 (GRCh37/hg19) (hg19)
- Ran alignment using default settings and Human (Homo sapiens) (b37): hg19 as reference genome.
- Took approximately 2.5 Hours, uploaded the "accepted hits" topcoat file to the server.
- Imported hg19_genes.gtf into my library.
- Used the RNA-Seq->Cufflinks option.
- This took about 3 hours to complete.
- Downloaded the "Gene Expression File".
- Uploaded it the the Haynes Lab server.
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