What graphs and charts I can build from processing tuberculosis whole genome short-reads and contigs?
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6.7 years ago
vassialk ▴ 200

What graphs and charts I can build from processing tuberculosis whole genome short-reads and contigs? I have performed mapping/alignment and variant calling. Need to build charts and graphs and do some meaningful statistical analysis further.

tuber visualization sequencing wgs sequence • 1.6k views
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6.7 years ago
DG 7.3k

Well there are the obvious things you might want to look at in terms of genomic resquencing in general like depth of coverage, breadth of coverage, etc. Basically how much sequencing data do you have in comparison to the reference genome you were mapping against. Basically how well have you covered the genome with sequencing data and some stats that relate to how accurate and confident you will be in your variant calling. In the case of de novo assemblies there are entirely different stats but you referenced mapping/alignment so I am assuming you are comparing to a reference sequence.

Otherwise you are looking at this problem backwards. You shouldn't be asking "what statistics can I do" or what nice looking fancy graphs can you make. You should be asking about the biological questions. What are you looking to get out of this data? What biological questions are you seeking to answer by sequencing these genomes and doing variant calling? Start from that point and then decide what statistics, analyses, and graphs you need to generate to answer or support those questions and hypotheses.

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"Otherwise you are looking at this problem backwards. You shouldn't be asking "what statistics can I do" or what nice looking fancy graphs can you make. You should be asking about the biological questions." This!

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Thanks Michael.

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