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Forum: Bioinformatics 07-21-2014, 06:45 PM
Replies: 16
Views: 7,006
Posted By me_myself_andI
In a nutshell: the one with more negative dG is...

In a nutshell: the one with more negative dG is more stable.

Andreas
Forum: Bioinformatics 07-21-2014, 06:37 PM
Replies: 16
Views: 7,006
Posted By me_myself_andI
Delasa, no offense meant, but you should really...

Delasa, no offense meant, but you should really do some background reading first. This is most basic (Bio)physics and needed to understand how any of this works.

Andreas
Forum: Bioinformatics 04-20-2014, 08:16 PM
Replies: 16
Views: 7,681
Posted By me_myself_andI
Hi Joe, I'm sorry, but currently available...

Hi Joe,

I'm sorry, but currently available versions of LoFreq can only predict substitutions, but not indels (see earlier post in this thread). Version 2.1 of LoFreq will be able to predict indels...
Forum: Bioinformatics 01-23-2014, 05:34 PM
Replies: 5
Views: 7,631
Posted By me_myself_andI
Yes, that's right!

Yes, that's right!
Forum: Bioinformatics 05-14-2013, 05:36 AM
Replies: 7
Views: 1,488
Posted By me_myself_andI
Shameless plug: one option is to simply not...

Shameless plug: one option is to simply not filter for mapping quality, and instead to use a low frequency variant caller that builds mapping quality into its model, e.g. LoFreq...
Forum: Bioinformatics 04-01-2013, 12:37 AM
Replies: 1
Views: 2,192
Posted By me_myself_andI
You might want to check out FreeBayes...

You might want to check out FreeBayes (http://bioinformatics.bc.edu/marthlab/FreeBayes), and possibly SNVer (http://snver.sourceforge.net/) or LoFreq (http://sourceforge.net/p/lofreq/wiki/Home/)
...
Forum: Bioinformatics 02-18-2013, 09:38 PM
Replies: 2
Views: 1,748
Posted By me_myself_andI
I would second the downsampling approach. ...

I would second the downsampling approach.

The removal of duplicates can in theory and depending on your setup introduce some biases. For example if your looking at subpopulations in viral or...
Forum: Bioinformatics 01-29-2013, 06:29 PM
Replies: 16
Views: 7,681
Posted By me_myself_andI
Hi ZL, when you change the Q parameter, you...

Hi ZL,

when you change the Q parameter, you filter all bases, i.e. reference and non-reference bases. This is not necessarily what you want. Qualities are built into LoFreq's model. By filtering...
Forum: Bioinformatics 01-28-2013, 12:36 AM
Replies: 16
Views: 7,681
Posted By me_myself_andI
Hi Wengkhong, it's not expected, but you can...

Hi Wengkhong,

it's not expected, but you can safely ignore those messages. It's actually a bug in one of the routines checking the integrity of the data. The data is fine, so don't worry. This is...
Forum: Bioinformatics 01-21-2013, 09:17 PM
Replies: 16
Views: 7,681
Posted By me_myself_andI
Hi WK, an alias won't work, because as...

Hi WK,

an alias won't work, because as LoFreq will use a system call to execute samtools. It therefore will use samtools found in the first path mentioned in your PATH variable.
Can you make sure...
Forum: Bioinformatics 10-29-2012, 11:46 PM
Replies: 2
Views: 1,240
Posted By me_myself_andI
Hard to say without giving us more info. The...

Hard to say without giving us more info. The unaligned version looks like it was downloaded from RDP. The other one doesn't, so I presume it was produced with some program. Then the dots could mean...
Forum: Bioinformatics 10-14-2012, 07:00 PM
Replies: 16
Views: 7,681
Posted By me_myself_andI
Hi all, we've released version 0.3.1, which...

Hi all,

we've released version 0.3.1, which is much easier to use. The most visible changes are: Samtools is now called internally, support for regions (bed), chromosome awareness (overdue) and a...
Forum: Bioinformatics 09-17-2012, 12:47 AM
Replies: 5
Views: 1,322
Posted By me_myself_andI
Hi, this is most likely due to samtools BAQ...

Hi,

this is most likely due to samtools BAQ computation. Briefly, it will downgrade base-qualities if a misalignment/indel is likely and that will change depending on the reference. See 2021320865...
Forum: Bioinformatics 07-16-2012, 01:12 AM
Replies: 1
Views: 4,654
Posted By me_myself_andI
Samtools uses Fisher's exact test. Input are the...

Samtools uses Fisher's exact test. Input are the base-counts of ref and alt bases from both strands.

See this post from the samtools mailing list...
Forum: Bioinformatics 07-11-2012, 11:31 PM
Replies: 16
Views: 7,681
Posted By me_myself_andI
Hi all, please note: we've moved the project...

Hi all,

please note: we've moved the project over to Sourceforge (https://sourceforge.net/p/lofreq/)
and also updated to a new version (much faster, lots of bug-fixes etc)

Andreas
Forum: Bioinformatics 07-02-2012, 12:42 AM
Replies: 1
Views: 3,408
Posted By me_myself_andI
Just a guess: you might be running out of memory....

Just a guess: you might be running out of memory. If that is the case, you might want to try --mergesort, but I'm not sure if this works in conjunction with --usersort.

Andreas
Forum: Bioinformatics 06-13-2012, 07:48 AM
Replies: 16
Views: 7,681
Posted By me_myself_andI
Hi, No need to split the fasta file. Just...

Hi,

No need to split the fasta file. Just run the Samtools/LoFreq combo once for each fragment, each time providing the corresponding fragment name to samtools, so that the [m]pileup is created...
Forum: Bioinformatics 06-13-2012, 04:22 AM
Replies: 16
Views: 7,681
Posted By me_myself_andI
Hi Mark, I'm afraid it doesn't at the...

Hi Mark,

I'm afraid it doesn't at the moment. I'm not sure, but I think FreeBayes might be able to handel indels.

Andreas
Forum: Bioinformatics 06-11-2012, 03:01 AM
Replies: 5
Views: 7,631
Posted By me_myself_andI
I think you might have to create the dict file...

I think you might have to create the dict file manually depending on the GATK version. I see this happening every now and then as well. The extra-complication is that if (my version of) GATK can't...
Forum: Bioinformatics 05-21-2012, 08:19 PM
Replies: 7
Views: 5,385
Posted By me_myself_andI
I might be wrong, but I think -d will only affect...

I might be wrong, but I think -d will only affect the pileup output, but not the snp prediction.
Forum: Bioinformatics 03-20-2012, 02:03 AM
Replies: 16
Views: 7,681
Posted By me_myself_andI
Low frequency variant caller for any ploidy level

Hi all,

we've developed a generic, sensitive and fast method (quite a mouthful but it's true, see for yourself :)) for prediction of very rare variants called LoFreq and I'd be happy if other...
Forum: Bioinformatics 02-28-2012, 10:52 PM
Replies: 1
Views: 3,041
Posted By me_myself_andI
Hi, I don't think there is an easy answer to...

Hi,

I don't think there is an easy answer to your problem. How do you define a SNP in this case? Do you have an external reference or is it part of your alignment?

And apart from that:
How...
Forum: Bioinformatics 09-12-2011, 02:53 AM
Replies: 21
Views: 7,703
Posted By me_myself_andI
Hi, you could give RazerS...

Hi,

you could give RazerS (http://www.seqan.de/projects/razers.html) (part of Seqan) or Mosaik (http://bioinformatics.bc.edu/marthlab/Mosaik) a try. RazerS for example let's you specify an...
Forum: Bioinformatics 09-06-2011, 04:42 AM
Replies: 16
Views: 7,006
Posted By me_myself_andI
Hi Raja, can't check this right now, but as...

Hi Raja,

can't check this right now, but as far as I remember RNAPlfold will not produce any other files than this postscript file. However, you can easily extract base pairing probabilities from...
Forum: Bioinformatics 06-20-2011, 10:12 PM
Replies: 4
Views: 1,264
Posted By me_myself_andI
In the case of RNA you could probably use ...

In the case of RNA you could probably use Infernal (http://infernal.janelia.org/) and an Rfam (http://rfam.sanger.ac.uk/) model of your choice to align it against your RNA in question.


Andreas
Showing results 1 to 25 of 30

 


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