Question: Comparative Genome Analysis on two or more draft bacterial genomes
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gravatar for xinsheng.zheng
5.6 years ago by
xinsheng.zheng0 wrote:

I had sequenced 2 bacterial genomes using Illumina platform. The genomes were assembled and annotated which allows me to view the genetic distribution of the genomes accross my samples using SeedViewer in RAST. However, I am now interested in finding the SNPs that present among these two genomes. I was suggested with MUMmers and MAUVE. I managed to reorder the contigs with closely related complete genomes from the database using MAUVE. Unfortunately, I can't perform SNPs call using MUMmers since both of my draft genomes contains multiple contigs instead of one as it shows error during the run. I was told that MAUVE can generate pseudogenomes which allows MUMmers to perform side to side genome comparison but I have not idea which data to choose since there are few files being generated by MAUVE. My question is, if there any tools which can generate a pseudo- single contig genomes (like the complete genome sequence) which ease the process of genomic analysis? If no, what are the strategy I should use in order for me to perform SNPs analysis on two draft genomes? My goal of the comparison is to find out the SNPs that present and its respected genes affected. Another question I would like to know is, what is the possible method to create a circular genome using draft genome data? Thank you.

snp next-gen genome • 1.9k views
ADD COMMENTlink modified 5.5 years ago by arpa53020 • written 5.6 years ago by xinsheng.zheng0
0
gravatar for h.mon
5.6 years ago by
h.mon32k
Brazil
h.mon32k wrote:

You can use Mauve directly to call SNPs: Mauve outputs a file with positions and bases for every polymorphic site (Mauve manual calls this file "the SNP file").

ADD COMMENTlink written 5.6 years ago by h.mon32k
0
gravatar for arpa530
5.5 years ago by
arpa53020
India
arpa53020 wrote:

Hello!!!

I am recently planning to work on CNV data analysis on Bladder Cancer. Could you please let me know how shall I find the Bladder cancer CNV data. 

ADD COMMENTlink written 5.5 years ago by arpa53020

It will be more useful if you open a new discussion (question) for you as well as others. 

ADD REPLYlink written 5.5 years ago by venu6.7k
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