Question: export consensus sequence
0
gravatar for taehyunp227
3.4 years ago by
taehyunp2270 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
ADD COMMENTlink written 3.4 years ago by taehyunp2270

What do you mean with consensus sequence in this regard?

ADD REPLYlink written 3.4 years ago by Bjoern Gruening5.1k

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 REPLYlink written 3.4 years ago by taehyunp2270
0
gravatar for Bjoern Gruening
3.4 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k 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 COMMENTlink written 3.4 years ago by Bjoern Gruening5.1k

Bjoern,

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

Taehyun

ADD REPLYlink written 3.4 years ago by taehyunp2270
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