Yaamini’s Notebook: Gonad Methylation Analysis Part 10

Visualizing bismark outputs

I started my IGV trials and tribulations yesterday, and today I’m (maybe) struggling a little less.

My goal was to use IGV to visualize 1) my alignment output and 2) bedGraphs from methylation extraction.

Alignment output

To visualize the alignment output, I first needed to sort and index the .bam output. I downloaded igvtools. In this lab notebook, I applied the sort and index command to one of my .bam files. I then uploaded this file to my IGV file.

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Figure 1. IGV with .bam file.

I had to zoom to the single nucleotide level to view anything!

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Figure 2. Alignment at single nucleotide level.

I wanted to add in my other alignment files, but I didn’t want to go through the pain of writing individual lines of code to convert the files (Sam tried to help me, but right now there doesn’t seem to be a solution. Steven also mentioned that I should have used deduplicate_bismark after the alignment, which would have sorted and indexed all my files. You can see the issue here).

bedGraphs

I uploaded all of the bedGraphs from the methylation extractor (found here) into my IGV file.

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Figure 3. bedGraphs showing methylation levels for each file.

There isn’t any apparent difference between the two treatments. I looked at Steven’s lab notebook and he noticed the same thing. He also said that going to 100k made a difference. I have no idea what this means so I’ll have to ask him.

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