Mouse lncRNA Brain Map Project Data and Analysis

• = TopHat 2.0.11

• = Cufflinks 2.2.1

• = cummeRBund 2.2

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?

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.