I have around 30 k sequences and need to find the codon frequencies how to deal with the presence of Ns in the sequence
should i need to mask the regions or to replace with specific nucleotides will this manipulate my results or try any other method to address this issue
This is not a sequencing data these are individual gene sequences downloaded from Ensembl I want to actually perform a chaos game representation on the sequences I did not know how to deal with the N s in the sequence
I need to make CGR(chaos game representation) matrix using gene sequences(~30k) these sequences were retrieved from Ensembl using Biomart I initially though codon usage shall compute similar to CGR thats why I initially mentioned about codon usage but in actual sense I hope CGR works different from codon frequency calculation so all I need is a CGR matrix for each of my sequence but several softwares and programs only produce image files and not a matrix so how could I do this also how deal with Ns in the sequences most programs are deleting the Ns but is this a correct approach
Sorry to offend you my work is pretty complex that I am unable to explain it properly I shall explain it as much as I can
I need to generate CGR(Chaos Game Representation) matrix for each of my gene sequence(~30k) the matrix should consists of the frequency of every nucleotide triplets ie AAA AAT AAG AAC .....................GGG on the column headers and the corresponding frequency in the columns in the form of a matrix
I tried using mEmboss ---> chaos software and used a python script provided in the url
https://bostjan-cigan.com/chaos-game-representation-of-gene-structure-in-python/
both the programs gave me output in the form of image either as sprinkled dots form or as a table with the frequencies (attached a sample image file) how to get the matrix
Also the gene sequence consists of Ns how to handle those Ns other programs delete Ns but is it biologically significant
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