Next steps in C.virg analysis

[yaaminiv]

I successfully completed all steps of bismark with a subset of my data.

Jupyter notebook
Lab notebook: Genome preparation, Alignment, Methylation Extractor and Report Generation

What are the next steps? Should I start to run the pipeline with the full extent of my sequencing data? How do I visualize all of the outputs?

[sr320]

Install methylkit and Macau (review manuals) From Bismark - data such as aligned reads (in reports) should be described - several graphs are generated

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On Sun, Apr 29, 2018 at 7:29 PM Yaamini Venkataraman < ***@***.***> wrote: I successfully completed all steps of bismark with a subset of my data. Jupyter notebook <https://github.com/RobertsLab/project-virginica-oa/blob/master/notebooks/2018-04-27-Gonad-Methylation-Bismark.ipynb> Lab notebook: Genome preparation <https://yaaminiv.github.io/Gonad-Methylation-Analysis-Part4/>, Alignment <https://yaaminiv.github.io/Gonad-Methylation-Analysis-Part5/>, Methylation Extractor and Report Generation <https://yaaminiv.github.io/Gonad-Methylation-Analysis-Part6/> What are the next steps? Should I start to run the pipeline with the full extent of my sequencing data? How do I visualize all of the outputs? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#239>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEPHt4cQ0DlH1UVRMS03Vw-_6YYYx-2Bks5ttnbbgaJpZM4TsEPS> .

[yaaminiv]

For bismark: Should just look at .txt file/HTML reports, or should I also open .bam files?

[sr320]

You should be familiar with what all output files are and what they are used for (see manual). Visualizing bedgraphs and bams has value.

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On Sun, Apr 29, 2018 at 11:54 PM Yaamini Venkataraman < ***@***.***> wrote: For bismark: Should just look at .txt file/HTML reports, or should I also open .bam files? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#239 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEPHt9SLFBnn-O9fNwSRvcWvQLOQ20-Iks5ttrTzgaJpZM4TsEPS> .