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Question: export consensus sequence
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gravatar for taehyunp227
3.4 years ago by
taehyunp227 • 0
taehyunp227 • 0 wrote:

Hi,

I have been using Galaxy.org for a couple of months now. It is such a powerful platform.

I have two questions regarding the consensus sequence. I was able to MAP with BWA using my NGS data against reference genome. At this point, how can I export the consensus sequence to use for the blast? Or should I use another command to get the consensus sequence from SAM file? Second question is which command should I use to do de novo alignment with NGS data without using the reference genome ?

Many thanks!

TP

 
bwa alignment galaxy • 1.7k views
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written 3.4 years ago by taehyunp227 • 0

What do you mean with consensus sequence in this regard?

ADD REPLY • link written 3.4 years ago by Bjoern Gruening ♦ 5.1k

I used Tablet to visualize SAM file. In Tablet, a contig contains all the reads and I figure out a "consensus" sequence manually. I want to be able to extract this consensus sequence automatically so I can do Blast with it. Thank you, Taehyun

ADD REPLY • link written 3.4 years ago by taehyunp227 • 0
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gravatar for Bjoern Gruening
3.4 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Assuming you mean, concatenated reads ... you can convert BAM to BED -> merge all overlapping BED regions with mergeBED and extract the sequence from those overlapping regions with "extract sequences from ..." tool.

Hope this helps,

Bjoern
ADD COMMENT • link written 3.4 years ago by Bjoern Gruening ♦ 5.1k

Bjoern,

I will try your suggestion and let you know. Thank you,

Taehyun

ADD REPLY • link written 3.4 years ago by taehyunp227 • 0
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