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Old 01-23-2019, 04:00 AM   #1
princethewinner
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Location: Delhi, India

Join Date: Jan 2019
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Question Genome Assembly vs Reference Genome for slicing around mutation location

Hello friends,


I have a bam file and corresponding vcf file from some source. I am trying to slice the DNA across its mutation location to feed into one of the algorithms.

I wanted to know what is the right way to do this. I have two options in my mind

1. I can create a genome assembly/contigs from the bam file and then slice it using mutation information from vcf file.

2. I can take a reference genome and then slice it using mutation information from vcf file.

What are the pros and cons of either method?

Any other suggestions to do the same is also appreciated.
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genome assembly, mutations, reference genome, rnaseq data

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