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- Like any good research story - one question always leads to another, and one answer opens up the rabbit hole of unending possibilities
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- And this is where the ensuing chapter arrives. Let's call it "[guppy](https://denbi-nanopore-training-course.readthedocs.io/en/latest/basecalling/basecalling.html)"!
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## Chapter II - Running 'methylation-aware' basecalling to improve the otherwise dismal sequencing error rates from ONT
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## Chapter II - Running `methylation-aware` basecalling to improve the otherwise dismal sequencing error rates from ONT
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- Installed guppy as follows:
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```
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# Installation
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less default.log
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```
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## Chapter III - What about 'non-methlyation-aware' basecalling, a.k.a. "non-mod" basecalling?
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## Chapter III - What about 'non-methlyation-aware' basecalling, a.k.a. `non-mod` basecalling?
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- The question arose as to what effect this might have
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- What better way to answer this, than test it?!
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```
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#########################
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### NO_MOD_basecalled ###
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#########################
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- Running the basecalled data that was generated without any "modifications" or "methylation-awareness"
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- Running the basecalled data that was generated `without` any "modifications" or "methylation-awareness"
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- To do this, we first have to move the "results" folder to a new name
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- then create a new "results" and keep the "basecalled_NO_MOD", but rename this folder to "basecalled"
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- Can be done via script as follows:
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| ... | ... | @@ -190,8 +190,8 @@ cat lr/GDB_2018_metaT_reads-x-barcode07-flye_contigs.avg_cov.txt | awk '{x+=$2; |
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#30.7486
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```
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## Chapter VI - the "big kahuna"
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- This part of the story is very much "serendipitous"
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## Chapter VI - the ``big kahuna``
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- This part of the story is very much `serendipitous`
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- Having a 1200 line Snakefile can be amazing; unless, for some unknown reason the entire run is triggered even when files are present
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- Due to this slight inconvenience of time, we decided to break down the Snakefile into "modular" sections
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- All the rules were broken down to [rules](https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab/-/tree/checkpoint_snakefile/2019_GDB%2Frulesurl) and [workflows](https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab/-/tree/checkpoint_snakefile/2019_GDB%2Fworkflowsurl)
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| ... | ... | |
