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