Gonad Methylation Analysis Part 6

The end of a pipeline test

Yesterday I encountered a gunzip error when aligning sequences with bismark. I opened a issue and documented everything in my lab notebook post. Steven said that I shouldn’t worry about it because I got .bam files! Today, I moved on in my Jupyter notebook to the bismark_methylation_extractor step. I successfully used the following parameters:


Once again, I encountered a gunzip error:


And like last time, I have outputs! You can find them in this folder. I ignored the error and moved on in the pipeline to the bismark2report step.

This step is fairly simple if you don’t want to customize the command. I used the following parameters:

  1. Path to bismark2report
  2. –dir + path to output directory

The reports generated can be found in this folder.

The last part of the pipeline is bismark2summary. I’m not sure how this differs from bismark2report, but I’m gonna use it anyways. It generated a report that can be found as a .txt file and .html report.

The next steps are to understand the outputs and start the full pipeline. I posted this issue to get Steven’s advice.

Written on April 29, 2018