Content Comparison

All these steps have already been run. We'll be spending time looking at the commands and output. Let's get set up.

Get the data

Step 1: Run tophat2

We've already gone over how this is done and looked over the results. Let's move on to step 2. 

 Step 2: Run cufflinks

cufflinks [options] <hits.bam>

Some of the important options:
	
 

Look at $BI/ngs_course/tophat_cufflinks/run_commands/cufflinks.commands to see how it was run.

Take a minute to look at the output files produced by one cufflinks run.

The important file is transcripts.gtf, which contains Tophat's assembled junctions for C1_R1.

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Step 3: Merging assemblies using cuffmerge

Create We first create a file listing the paths of all per-sample transcripts.gtf files so far, then pass that to cuffmerge:

cd $BI/ngs_course/tophat_cufflinks
find . -name transcripts.gtf > assembly_list.txt
cuffmerge <assembly_list.txt>

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