CNVanalysis

Prerequirements

We need to download CNVpytor, Samtools, and other necessary files for smooth processing of the CNV analysis.

Installing the CNVpytor and Samtools

For installing and setup of the CNVpytor follow the below steps :

pip install cnvpytor
#add path of cnvpytor if needed
cnvpytor -download

We will also be needing samtools so for that, follow the below steps:

sudo apt-get -y samtools

Downloading reference genomes or required genome files.

It is expected that the sequence files will be there in a single folder. which contains reference genome. For downloading we can simply use the wget function.

wget <reference genome link>
wget https://hgdownload.soe.ucsc.edu/goldenPath/ce11/bigZips/ce11.fa.gz

wget <links of sequence files>

need of conf file for refernce

We need a configuration file for each reference species. Here we are working on C. elegans. So I have already uploaded it. It can be downloaded using:

wget https://github.com/Rajarshi0/CNVanalysis/blob/main/ce11_ref_genome_conf.py

Creating the gc file

For creating the gc file we need the the unzipped fasta sequence of the sequence (here, reference). I have given syntax for C. elegans:

gzip -d ce11.fa.gz > ce11.fa
cnvpytor -root ce11_gc_file.pytor -gc ce11.fa -make_gc_file

I hope after this the script will run smoothly. It is uploaded here only. Thank you so much