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Search: Posts Made By: dagarfield
Forum: Bioinformatics 03-19-2016, 07:28 AM
Replies: 62
Views: 25,510
Posted By dagarfield
Post the problem anyways. Someone may reply.

Post the problem anyways. Someone may reply.
Forum: Bioinformatics 11-24-2015, 03:17 AM
Replies: 62
Views: 25,510
Posted By dagarfield
The -m any option

Hello!

A quick question about your "-m any" option.
In rare instances, the Nextera kits can give you sequences that look a bit as follows:
...
Forum: Sample Prep / Library Generation 01-15-2015, 01:39 AM
Replies: 20
Views: 21,435
Posted By dagarfield
We've not yet tried this, but I'm considering it...

We've not yet tried this, but I'm considering it -- it sure would be nice to barcode during the Tagmentation step rather than the PCR step....if someone tries this, there's a beer in it for you at...
Forum: Sample Prep / Library Generation 05-03-2014, 11:57 PM
Replies: 20
Views: 21,435
Posted By dagarfield
It seems to work just fine: If you can see your...

It seems to work just fine: If you can see your post-PCR product on a gel, you'll have a fine library (in our experience). Some of the runs have more mtDNA reads than you would expect from, say,...
Forum: Sample Prep / Library Generation 05-03-2014, 09:12 AM
Replies: 20
Views: 21,435
Posted By dagarfield
Works just fine. :)

Works just fine. :)
Forum: Sample Prep / Library Generation 03-24-2014, 05:27 AM
Replies: 20
Views: 21,435
Posted By dagarfield
Many thanks, this looks great. I'll update the...

Many thanks, this looks great. I'll update the thread with progress.
Forum: Sample Prep / Library Generation 03-20-2014, 01:16 AM
Replies: 20
Views: 21,435
Posted By dagarfield
Tagmentation DNA Buffer (TD)

Hey folks,

This seems a slim chance, but here goes: Does anyone have a recipe for the DNA Tagmentation Buffer that comes with Nextera DNA Sample Preparation Kit? We've found it helpful to wash our...
Forum: Bioinformatics 09-03-2013, 04:43 AM
Replies: 4
Views: 20,813
Posted By dagarfield
Maybe this will be useful? ...

Maybe this will be useful?

https://code.google.com/p/bedops/wiki/vcf2bed
Forum: Bioinformatics 09-20-2012, 10:35 PM
Replies: 9
Views: 8,809
Posted By dagarfield
I think this problem of indels has been at least...

I think this problem of indels has been at least partially addressed using mpileup. That said, I've heard good things about the route James is recommending.
Forum: Bioinformatics 09-06-2012, 07:00 AM
Replies: 3
Views: 2,457
Posted By dagarfield
In the end, I went with a hybrid approach of...

In the end, I went with a hybrid approach of writing a few scripts of my own plus one that translates a vcf to a phylip (or hapmap) file so that the data can be processed by VariScan. In truth this...
Forum: Bioinformatics 07-27-2012, 07:55 AM
Replies: 3
Views: 2,457
Posted By dagarfield
VCF to pseudo BAM

I've an odd question.
I'm working with a set of VCF files from multiple individuals in a population. However, there are a number of tools for population genetic analyses (e.g. popbam) that take BAM...
Forum: Bioinformatics 07-27-2012, 07:48 AM
Replies: 3
Views: 1,642
Posted By dagarfield
Any news on this front? It looks like the...

Any news on this front?

It looks like the next version of VCFtools will include Tajima's D (and may already have estimates like pi -- check out the patches), but nothing besides POPBAM currently...
Forum: Bioinformatics 10-18-2011, 07:20 AM
Replies: 0
Views: 2,983
Posted By dagarfield
An example, multi-sample VCF file?

Hiya folks,

Does anyone have a multi-sample VCF file (or at least a portion of one) that they'd be willing to share with me? I'm trying to convert some non-VCF formatted data to VCF format so that...
Forum: Bioinformatics 05-27-2011, 08:12 AM
Replies: 5
Views: 4,294
Posted By dagarfield
I just ran mine with the following syntax ...

I just ran mine with the following syntax

samtools mpileup -f myGenome.fasta myBam.bam > myoutput.txt

Where myGenome.fasta is a fasta file on which I have run the command

samtools faidx...
Forum: Bioinformatics 05-26-2011, 09:47 AM
Replies: 5
Views: 4,294
Posted By dagarfield
It is not obvious to me where that information is...

It is not obvious to me where that information is in the VCF file, if it is in there at all. However, you might be able to get something in the file generated by mpileup.

Rather than generating a...
Forum: Bioinformatics 05-25-2011, 04:55 PM
Replies: 3
Views: 5,420
Posted By dagarfield
I was thinking specifically of this option ...

I was thinking specifically of this option

-1 FLOAT min P-value for strand bias (given PV4) [0.0001]

Strand bias is not something I've thought much (at all) about, but this option seems like...
Forum: Bioinformatics 05-25-2011, 04:52 PM
Replies: 5
Views: 4,294
Posted By dagarfield
As I understand it, we shouldn't be using pileup...

As I understand it, we shouldn't be using pileup anymore. Yes, the output is nice, but all of the same information is (somewhere) in the VCF file.

As for what's being filtered out, however, I...
Forum: Bioinformatics 05-25-2011, 04:47 PM
Replies: 3
Views: 5,420
Posted By dagarfield
Maybe vcfutils.pl varFilter?

Maybe vcfutils.pl varFilter?
Forum: Bioinformatics 05-25-2011, 04:41 PM
Replies: 3
Views: 5,614
Posted By dagarfield
I think you may find this link helpful ...

I think you may find this link helpful
http://samtools.sourceforge.net/mpileup.shtml

Pileup is now depreciated.
Forum: Bioinformatics 03-09-2011, 06:43 AM
Replies: 13
Views: 4,154
Posted By dagarfield
How much coverage do you have? If you have low...

How much coverage do you have?
If you have low coverage, and you're predicting transcripts de novo, cufflinks is going to give you a lot of transcripts (because many of your reads don't overlap...
Forum: Bioinformatics 03-09-2011, 06:41 AM
Replies: 5
Views: 6,651
Posted By dagarfield
Oh, all kinds of good things. More from Heng Li. ...

Oh, all kinds of good things. More from Heng Li.




And from Manuel Rivas at the Broad



Manuel distinguishes between Syzygy and GATK
Forum: Bioinformatics 03-09-2011, 05:43 AM
Replies: 5
Views: 6,651
Posted By dagarfield
Another response from Heng Li on the samtools...

Another response from Heng Li on the samtools help list
Forum: Bioinformatics 03-09-2011, 04:07 AM
Replies: 5
Views: 6,651
Posted By dagarfield
Here's a response I got from the samtools mailing...

Here's a response I got from the samtools mailing list...not overly encouraging for Samtools for this problem. Any suggestions for other good SNP calling programs?
Forum: Bioinformatics 03-08-2011, 04:37 PM
Replies: 5
Views: 6,651
Posted By dagarfield
Calling tri-allelic SNPs using samtools (or similar)

Hi folks,

We work with sea urchin larvae in our lab. They are very, very, very tiny and, thus, we need to collect a whole bunch of them at a time to get sufficient starting material for NGS....
Forum: Bioinformatics 03-08-2011, 09:53 AM
Replies: 0
Views: 2,823
Posted By dagarfield
Understanding the -d -D and -S options on samtools mpileup

Hi folks,

I've just upgraded our samtools after finding, to my delight, that there have been improvements/changes/additions to the package that make it possible to generate consensus sequences...
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