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Search: Posts Made By: drio
Forum: Bioinformatics 02-11-2011, 08:46 AM
Replies: 3
Views: 2,605
Posted By drio
If I am not mistaken the latest version uses the...

If I am not mistaken the latest version uses the SOAP model instead of the MAQ model at the core of the snp caller. Let us know if by removing BAQ computations (-B) you get similar results to the old...
Forum: Bioinformatics 02-11-2011, 07:19 AM
Replies: 3
Views: 2,605
Posted By drio
The snp caller engine has changed dramatically...

The snp caller engine has changed dramatically among those versions. Review carefully the manuals (http://samtools.sourceforge.net/), particularly mpileup...
Forum: Events / Conferences 02-09-2011, 04:35 AM
Replies: 8
Views: 16,170
Posted By drio
You are right this year there were not big...

You are right this year there were not big announcements. There were some memorable talks (Rob Knight comes to my mind). But, as usual, the best of AGBT is the networking and being able to hang out...
Forum: Bioinformatics 02-08-2011, 02:33 PM
Replies: 1
Views: 1,118
Posted By drio
If you want to do it by hand, explore the...

If you want to do it by hand, explore the --prefix option in most configures. That will help you if the package you are working on follows some open sources basic standards.

Also, for alignments,...
Forum: General 01-31-2011, 05:35 PM
Replies: 1
Views: 1,429
Posted By drio
Can you add -U and try again?

Can you add -U and try again?
Forum: SOLiD 01-26-2011, 04:49 AM
Replies: 40
Views: 8,693
Posted By drio
I think the reason for not having a minicluster...

I think the reason for not having a minicluster is the use of FPGAs along with a very powerful machine (like illumina). Anyone has more info about that? I guess we'll find out at AGBT.
Forum: SOLiD 01-21-2011, 04:19 AM
Replies: 2
Views: 1,822
Posted By drio
1. Take a screenshot of IGV for that region and...

1. Take a screenshot of IGV for that region and send it over to ABi. They will tell you what's going on. You can also paste it here.

2. Typically ABi implements indel calling in a different...
Forum: Bioinformatics 01-17-2011, 06:55 AM
Replies: 9
Views: 11,121
Posted By drio
1. Tell your sysadmins to install R...

1. Tell your sysadmins to install R (http://www.r-project.org/) in your cluster/machine.

2. Change jvm-args for whatever parameters you want to use. Typically: -Xmx2g for
picard.
Forum: Bioinformatics 01-13-2011, 01:39 PM
Replies: 5
Views: 2,134
Posted By drio
Consider uploading your data to the cloud (Amazon...

Consider uploading your data to the cloud (Amazon and others) and instantiate as much computer power as you need.
Forum: Bioinformatics 01-13-2011, 04:59 AM
Replies: 4
Views: 2,426
Posted By drio
Also take a look to dnaa...

Also take a look to dnaa (http://sourceforge.net/apps/mediawiki/dnaa/index.php?title=Main_Page), specifically the dwgsim (forked from the maq tool).
Forum: Illumina/Solexa 01-12-2011, 03:59 AM
Replies: 1
Views: 1,187
Posted By drio
The Illumina pipeline is mainly C++ (heavily...

The Illumina pipeline is mainly C++ (heavily relying on the boost lib), perl, python and GNUMake. Using macports (http://www.macports.org/) you should be able to make it run.

Also, if you want to...
Forum: Bioinformatics 01-10-2011, 12:38 PM
Replies: 1
Views: 1,132
Posted By drio
If you want to generate SRFs for SOLiD data the...

If you want to generate SRFs for SOLiD data the solid2srf tool from ABi is the only one I know about.

I thought most of the submissions did not require intensities anymore. Are you sure you are...
Forum: Bioinformatics 01-10-2011, 02:20 AM
Replies: 2
Views: 1,473
Posted By drio
Dump your NA alignements in SAM and inspect the...

Dump your NA alignements in SAM and inspect the 5th bit of the second field of your alignments.
Forum: Bioinformatics 01-07-2011, 02:29 AM
Replies: 4
Views: 2,505
Posted By drio
I suggest you follow the lessons...

I suggest you follow the lessons (http://mkweb.bcgsc.ca/circos/tutorials/lessons/) from the site. Each lesson has code and the results of the images. Plot is complicated because it is very flexible...
Forum: Bioinformatics 01-05-2011, 01:01 PM
Replies: 14
Views: 2,778
Posted By drio
sammy07, athomma, Could you please try the...

sammy07, athomma,

Could you please try the git version? That should fix the issue.


$ git clone git://bfast.git.sourceforge.net/gitroot/bfast/bfast
$ sh ./autogen.sh && ./configure && make ...
Forum: Bioinformatics 01-05-2011, 06:23 AM
Replies: 4
Views: 1,131
Posted By drio
Sometimes developers focus mainly in getting the...

Sometimes developers focus mainly in getting the tool up and running on the traditional OS and hardware, that's linux (The windows of this field :)) and x86.

I have to say there are many tools...
Forum: Bioinformatics 01-05-2011, 06:12 AM
Replies: 2
Views: 1,194
Posted By drio
Do you have any space left in the volumen where...

Do you have any space left in the volumen where BF is dumping the data?
Forum: Bioinformatics 01-04-2011, 02:30 AM
Replies: 6
Views: 1,444
Posted By drio
Can you show the files from within the reference...

Can you show the files from within the reference directory as well as the exact commands you run?

Is it possible you forgot to use -A1 to tell bfast to compute the local alignments in CS?
Forum: Bioinformatics 01-03-2011, 10:44 AM
Replies: 12
Views: 5,062
Posted By drio
Explore samtools reheader and picard's...

Explore samtools reheader and picard's ReplaceSamHeader (command line tools).
Check if they modify the RG field once you add your new header (with your RG).
I don't think they'll change it. In...
Forum: Bioinformatics 01-03-2011, 06:26 AM
Replies: 14
Views: 2,778
Posted By drio
Thanks for bringing this up (on this one thread)....

Thanks for bringing this up (on this one thread). Let me see if I can install a VM with fedora14 and reproduce the problem.
Forum: Bioinformatics 01-03-2011, 06:16 AM
Replies: 12
Views: 5,062
Posted By drio
Explore bfast's -r postprocessing option: ...

Explore bfast's -r postprocessing option:


-r RGFileName Specifies to add the RG in the specified file to the SAM
header and updates the RG tag (and LB/PU...
Forum: Bioinformatics 01-02-2011, 04:39 AM
Replies: 8
Views: 9,962
Posted By drio
Take a look to this...

Take a look to this (http://seqanswers.com/forums/showthread.php?t=8334) thread.

I'd suggest you follow bwa's FAQ advice and rely more in the MAPQ. Still, if you want to
filter uniquely mapped:...
Forum: Bioinformatics 12-27-2010, 07:04 AM
Replies: 15
Views: 7,467
Posted By drio
Try: $ samtools view -F5 merge.bam | awk...

Try:


$ samtools view -F5 merge.bam | awk '$3=="chr1"'| wc -l


That plus 2061072 should equal 2163811
Forum: Bioinformatics 12-27-2010, 05:44 AM
Replies: 15
Views: 7,467
Posted By drio
You mean the third column shows reads where both...

You mean the third column shows reads where both ends map and the forth column shows reads where one of the reads maps? Then, if working with single end data, both columns should display the same...
Forum: Bioinformatics 12-27-2010, 12:57 AM
Replies: 15
Views: 7,467
Posted By drio
BWA also picks a random alignment when there are...

BWA also picks a random alignment when there are multiple equally good matches. But, I am not sure how that is going to change those numbers from idxstats?

I am not sure what is the meaning of the...
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