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suranyivica / Msm_stress

This repository was created to share the pipeline and analysis of WGS data of Mycobacterium smegmatis.
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seqeunce of script #1

Open jloubser opened 1 year ago

jloubser commented 1 year ago

Hi!

I'd liek to try out the scripts, I have two isolates to analyze. Could you perhaps provide some documentation in terms of the sequence of the scripts. I can more or less figure it out but I'd just like to make sure?

Thank you!

suranyivica commented 1 year ago

Hi,

Thank you very much for contacting!

The seqeunce was the following:

1.Fastqc_script.sh 2.trim_script.sh (in case the reads needed to be trimmed) 3.analysis.sh (note, that the ploidy and sample names need to be adjusted) 4.vcf_work.sh 5.allele_frequency_filtering_for_unique_mut.py 6.mutation_analysis (either for 5 or 6 strains, depending on the actual file)

Hope this helps! Best, Eva