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```
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- however the need to re-run the same samples by swapping was not only cumbersome, but depending on the orientation of the samples, obtained non-overlapping sets of fasta list
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## So, I decided to pursue [mmseqs2](https://github.com/soedinglab/MMseqs2) instead
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# So, I decided to pursue [mmseqs2](https://github.com/soedinglab/MMseqs2) instead
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* The output of this is now incorporated into the [updated_SNAKEFILE](https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab/-/blob/master/2019_GDB/updated_SNAKEFILE) that will be used for the analyses going forward.
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* see also [MMSEQ_RULES](https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab/-/blob/master/2019_GDB/rules/MMSEQ_RULES) |
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\ No newline at end of file |
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* see also [MMSEQ_RULES](https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab/-/blob/master/2019_GDB/rules/MMSEQ_RULES)
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## And this is where the fun begins..
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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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- Installed guppy as follows:
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```
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# Installation
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cd /home/users/sbusi/apps
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wget https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy_research_rle_0.0.0_linux64.tar.gz
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tar -xzvf ont-guppy_research_rle_0.0.0_linux64.tar.gz
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export PATH=$PATH:"/home/users/sbusi/apps/ont-guppy/bin/"
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```
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- Basecalling with methylation-aware latest 'guppy' update
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```
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# first one has to make the appropriate directories
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cd /scratch/users/sbusi/ONT/
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mkdir cedric_ont_basecalling/
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cd /scratch/users/sbusi/ONT/cedric_ont_basecalling
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cp /scratch/users/claczny/ont/fecal_pilot_testing/cluster.json .
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cp /scratch/users/claczny/ont/fecal_pilot_testing/config.yaml .
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cp /scratch/users/claczny/ont/fecal_pilot_testing/Snakefile .
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cp /scratch/users/claczny/ont/fecal_pilot_testing/src/* .
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mkdir src && mv *.sh src/.
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# edited the above files as needed with correct paths (OR) do the following
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ln -sd /scratch/users/claczny/ont/fecal_pilot_testing/data data
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ln -sd /scratch/users/claczny/ont/fecal_pilot_testing/dbs dbs
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ln -sd /scratch/users/claczny/ont/fecal_pilot_testing/envs envs
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ln -sd /scratch/users/claczny/ont/fecal_pilot_testing/scripts scripts
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# basecalling run as follows after modifying the "rule all" inputs for basecalling.done
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./src/snakemake_run_use_conda.sh
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# individual snakemake rules can also be run separately as follows:
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snakemake -p --use-conda BASECALL_MERGE_QC
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snakemake -p --use-conda COVERAGE_OF_REFERENCES
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# LOG can be checked as follows:
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less default.log
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```
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##### GITLAB #####
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- copying all changed files to gitlab: https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab
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```
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cd /scratch/users/sbusi/ONT/cedric_ont_basecalling
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git pull https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab.git
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cd /scratch/users/sbusi/ONT/cedric_ont_basecalling/ont_pilot_gitlab
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cp ../Snakefile .
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git checkout work
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git add Snakefile
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git commit -m "any message of note"
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git push
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# go to the provided URL, and then submit the merge request, for it to be approved later.
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```
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##### SLURM files #####
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- moving all slurm files into one folder for 'cleaner' appearance
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```
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mkdir slurm_files
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mv slurm* slurm_files/.
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``` |
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\ No newline at end of file |
