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BrainMap

Mouse lncRNA Brain Map Project Data and Analysis

Dependencies

  • = TopHat 2.0.11

  • = Cufflinks 2.2.1

  • = cummeRBund 2.2

Overview

Workflow

  1. Aquire reads from sequencing runs
    • Aggregate .fastq files as needed for each library
  2. Align reads
    • Run alignReads.sh for each sample (read1 and read2 aggregate fastqs) to create aligned .bam
    • Update sample sheet with all information for a given sample included .bam location
  3. Define contrasts (generally WT vs KO for each strain)
  4. Run cuffdiff/cuffnorm
    • scripts/cuffdiff/cuffdiff_full.sh
  5. Analysis?

FASTQ Alignments

Cuffdiff run

CummeRbund analysis

To view the wt-v-ko sequencing reports for each timepoint for each strain, click "analysis" and then the appropriate folder.

Click the ".md" file to view the report in your browser. Print as a pdf to take it to go! If you'd like the individual images, those are located in the "figure" folder in each directory.