Question: Help! Obtaining consensus sequence from Aligned BAM file
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gravatar for liamwhitmore22
11 months ago by
liamwhitmore220 wrote:

Hi!

I have just aligned a paired-end FastQ (R1 & R2) files to a published viral genome using Bowtie2. The end goal is to extract the aligning reads from this sample and obtain a consensus sequence. Then I'd like to eventually compare that sequence to a reference sequence (published) to compare the differences between the two (I basically want to see if there is any nucleotide variation between the two samples), to help with primer design.

So, I have never done this type of pipeline before and would just like some assistance on creating and obtaining a consensus sequence. I use usegalaxy.eu and not coding.

Thanks!

tutorial assembly • 239 views
ADD COMMENTlink modified 10 months ago by Biostar ♦♦ 20 • written 11 months ago by liamwhitmore220
1

You can post this over at Galaxy help forum to get galaxy specific answers.

If you are able to replicate the steps in this tutorial on Galaxy then it should work: Generating consensus sequence from bam file

ADD REPLYlink written 11 months ago by genomax84k
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