Handling NGS data using IGV

Alarrisa

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Join Date: Jan 2018

Posts: 1
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Handling NGS data using IGV

01-30-2018, 02:24 PM

Good evening,

I do not work in bioinformatics, I have chosen a module in bioinformatics and completely out of my depth!
I have an assessment where I am given a reference bacterial genome in FastA format and a GFF file containing the annotations and the position of predicted genes.
I have illumine sequence reads generated by shotgun sequencing of genomes of several closely related bacteria.
The objective: identify interesting differences among the sequenced bacterial genomes!
I have no idea how to interpret this data. I started the module late due to personal reasons and I have 2 weeks to submit a poster with my findings!!

Can one or a few of you bioinformatics wizards help me out please?

Last edited by Alarrisa; 01-30-2018, 02:30 PM. Reason: it was wrong
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GenoMax

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Join Date: Feb 2008

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01-30-2018, 04:02 PM

Can you tell us what you have learned as a part of this module? Do you know what the raw data looks like? What needs to be done with it in terms of QC/clean-up? Do you know what sequence alignment is with reference to NGS data? Are you limited to certain tools? Are you allowed to use online tools?
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Handling NGS data using IGV

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