strand bias, gram negative bacteria

Question

[Nitha]

Hi,

I have chlamydia trachomaticsA genome, it consists 919 sequence and I am thinking to do strand bias. I checked online, it's showing ngs tool, like samtools, GATK etc. but I am searching any online tools other than NGS tool.

How can I do strand bias calculation for these 919 gene using GENE BANK?

Can anyone help me?

Thanks,
Nitha

[abascalfederico]

Nina, with "strand bias" do you refer to the distribution of genes on both strands or to the frequency of nucleotide bases?

BTW, why do you have so many sequences for the c. trachomatis genome? Are these different strains? A proper analysis of strand bias requires fully (or almost fully) assembled genomes. I would choose just one C. trachomatis genome to start with.

[Nitha]

Yes, I have to check strand bias for 3 strains genome of C. trachomatis A, B,C, to perform strand bias and check the bias in which strand, mostly its said the bias occur in leading strand, I have to check in which strand in my 3 strains genome. I don't want to use samtools or GATK, any other way to find most essential gene in these strain.. Any other method to perform.. Using codonW, i have got some results, I have to compare these results with strand bias results and select most essential gene. please help me to perform..