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How to generate consensus sequence for all refs (Read 13346 times)
Oct 6th, 2014 at 3:46pm

Sami   Offline
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Hi,

I have been trying to use samtools to create consensus sequences. However, it seems that conseqs.fastq (see command below) is missing consensus sequences for most reference sequences.

--- samtools command ---
samtools mpileup -uf ref.fa sorted.bam | bcftools view -cg - | /usr/share/samtools/vcfutils.pl vcf2fq > conseqs.fastq
----

In IGV, I can create consensus sequence for all references (one by one). I would like to create the consensus sequences with a command line tool.

I asked this question at seqanswers forum and got an answer that creating the consensus sequences is possible with UGENE command line.

Can I have an example of an UGENE command that can be used to build consensus sequences from ref.fasta and sorted.bam files?

Thanks
 
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Reply #1 - Oct 7th, 2014 at 5:38pm

Olga Golosova   Offline
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Hello,

In the current UGENE version 1.14.1 you can do the task only partially:

1) You can find out variants by a reference sequence and an assembly. It is the same as command:
Code:
samtools mpileup –uf <input_reference> <input_bam> | bcftools view –vg – | vcfutils.pl varFilter –D 100 


For details, see: Call Variants with SAMtools

2) You can find out a consensus sequence from an assembly.
For details, see: Extract Consensus from Assembly

Unfortunately, it is not possible to get a new sequence from a reference + variations combination. We will add this feature into the next major UGENE release 1.15. Here is the link to the corresponding request in our issue-tracking system: UGENE-3588
Note that any workflow in UGENE can also be run from the command line.
 
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Reply #2 - Dec 17th, 2015 at 4:23am

QTheory1   Offline
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Is the input still the same to do this in version 1.15 because I input that code and nothing happened.
 

You can see the members area for the wealthy affiliate now.
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Reply #3 - Dec 22nd, 2015 at 4:18pm

Olga Golosova   Offline
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Quote:
Is the input still the same to do this in version 1.15 because I input that code and nothing happened.

What do you mean? The workflow in UGENE is still the same. Do you mean the original SAMtools command line tool?
 
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Reply #4 - Dec 20th, 2016 at 4:09am

Claire Ellison   Offline
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Question: What Better Way To Get Consensus Sequence Of Mapping Against Reference Genome Using Samtools Mpileup?
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You can see the members area ADELE WEIGHT LOSS .
« Last Edit: Dec 27th, 2016 at 12:39am by Claire Ellison »  
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Reply #5 - May 22nd, 2018 at 7:02am

Priscilla Hamer   Offline
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I'm still using version 1.14.1 because I love this version so much that I never updated it. But I can't get a new sequence from a reference and variations combination in this version. What do you suggest? Should I upgrade to the latest version 1.29.0? Or is it possible to do so in any version above 1.14.1? If yes, where can I download it from?
 

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Reply #6 - May 22nd, 2018 at 9:08am

Olga Golosova   Offline
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Priscilla Hamer wrote on May 22nd, 2018 at 7:02am:
I'm still using version 1.14.1 because I love this version so much that I never updated it. But I can't get a new sequence from a reference and variations combination in this version. What do you suggest? Should I upgrade to the latest version 1.29.0? Or is it possible to do so in any version above 1.14.1? If yes, where can I download it from?

Thank you for the feedback, Priscilla!

Unfortunately, this feature is not yet available in UGENE 1.29.0 as well. Instead, you might use, for example, FastaAlternateReferenceMaker from GATK (in the command line).

We'll take into account your request and add this feature in one of the nearest UGENE versions.
 
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Reply #7 - Jun 25th, 2018 at 2:55pm

lexen luis   Offline
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I also use the version UGENE 1.14.1. And this version perfectly works  for me. Is there any updated version?
 
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Reply #8 - Jun 25th, 2018 at 3:00pm

Olga Golosova   Offline
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Hi lexen luis!

Yes, current UGENE version is 1.30. See a brief description of new features here: http://ugene.net/changelist.html.
 
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Reply #9 - Aug 21st, 2018 at 4:04pm

Brestrogen   Offline
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Priscilla Hamer wrote on May 22nd, 2018 at 7:02am:
I'm still using version 1.14.1 because I love this version so much that I never updated it. But I can't get a new sequence from a reference and variations combination in this version. What do you suggest? Should I upgrade to the latest version 1.29.0? Or is it possible to do so in any version above 1.14.1? If yes, where can I download it from?

 
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Reply #10 - Aug 22nd, 2018 at 3:40am

Lyman   Offline
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lexen luis wrote on Jun 25th, 2018 at 2:55pm:
I also use the version UGENE 1.14.1. And this version perfectly works  for me. Is there any updated version?


The UGENe has many updates after this the current stable version is 1.31.0 (August, 2018).
 
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Reply #11 - Aug 28th, 2018 at 9:33pm

Peyton12345   Offline
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Hello there you can do it in the current UGENE version 1.14.1 you can do the task only partially
 
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Reply #12 - Aug 29th, 2018 at 12:48am

shane   Offline
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Peyton12345 wrote on Aug 28th, 2018 at 9:33pm:
Hello there you can do it in the current UGENE version 1.14.1 you can do the task only partially


Thank for the help it would be really appreciable. Smiley
 
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Reply #13 - Aug 29th, 2018 at 8:35pm

Peytonn james   Offline
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is the input same of the version when ever i input something nothing happens
 
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