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Question: Bacterial Sequence for Variant Analysis
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gravatar for ppurkayastha2010
20 months ago by
ppurkayastha2010 • 30
ppurkayastha2010 • 30 wrote:

I am analyzing paired-end data for bacterial genome and have done the following steps:

*FASTQC analysis

*Trim Galore

*Bowtie2

I have got a BAM file after the alignment with reference sequence using Bowtie2.

Please let me know what are steps I should follow for variant analysis and to check the number of different mutations.
rna-seq snp • 1.1k views
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modified 20 months ago by m.bernt • 40 • written 20 months ago by ppurkayastha2010 • 30
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gravatar for m.bernt
20 months ago by
m.bernt • 40
m.bernt • 40 wrote:

The following tutorial might be a good starting point:

https://galaxyproject.org/tutorials/var_hap/
ADD COMMENT • link written 20 months ago by m.bernt • 40

How can the steps for human mitochondrial genome used for bacterial genome?

ADD REPLY • link written 20 months ago by ppurkayastha2010 • 30
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