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Search: Posts Made By: cwhelan
Forum: Bioinformatics 06-12-2013, 08:33 AM
Replies: 4
Views: 2,375
Posted By cwhelan
How big is the deletion you are looking for? Do...

How big is the deletion you are looking for? Do you have RNA-seq data or whole genome sequencing?

If you know exactly where it is you might try simply looking for discordant read pairs that map to...
Forum: Bioinformatics 03-21-2013, 10:49 AM
Replies: 1
Views: 1,916
Posted By cwhelan
Use the gem-2-sam program that comes with GEM to...

Use the gem-2-sam program that comes with GEM to turn it into SAM format.

http://algorithms.cnag.cat/wiki/The_GEM_library
Forum: Bioinformatics 02-25-2013, 08:09 AM
Replies: 15
Views: 4,945
Posted By cwhelan
My workflow usually goes like this: 1)...

My workflow usually goes like this:

1) convert calls to bedpe format (see the docs for BEDtools for examples)
2) use bedtools pairToPair to subtract germline SVs from the breakpoints from the...
Forum: Bioinformatics 01-10-2013, 09:30 PM
Replies: 2
Views: 1,906
Posted By cwhelan
This is normal although it should only happen in...

This is normal although it should only happen in a few regions. This paper suggests that it is due to misassembled regions of the reference where there should be many copies of a repeat but there's...
Forum: Genomic Resequencing 12-14-2012, 08:39 AM
Replies: 12
Views: 6,003
Posted By cwhelan
It's strange that that is taking so long for you;...

It's strange that that is taking so long for you; I don't think it took as long for me. I ran each fille in parallel on different cores, that's one way to speed it up.
Forum: Genomic Resequencing 12-12-2012, 09:16 AM
Replies: 12
Views: 6,003
Posted By cwhelan
Try using the -e and -a options for vcf-subset. I...

Try using the -e and -a options for vcf-subset. I believe that without those it still writes a line for every locus that has a variant, even if that variant is not present in the sample that you are...
Forum: Bioinformatics 12-04-2012, 08:47 AM
Replies: 7
Views: 4,464
Posted By cwhelan
I think that 46bp might be a bit large to detect...

I think that 46bp might be a bit large to detect with only a BWA/GATK pipeline. You can try increasing your -e parameter a lot in BWA, however.

With 150bp PE reads, I would suggest running your...
Forum: Bioinformatics 10-23-2012, 08:38 AM
Replies: 8
Views: 2,510
Posted By cwhelan
Yes, that's what I was going to suggest.

Yes, that's what I was going to suggest.
Forum: Bioinformatics 10-15-2012, 09:46 AM
Replies: 8
Views: 2,510
Posted By cwhelan
Yes, Breakdancer supports merged bam files from...

Yes, Breakdancer supports merged bam files from multiple libraries as long as the SAM header and records have all of the RG information for each library/read. I've had success using the bam2cfg...
Forum: Bioinformatics 09-05-2012, 10:23 AM
Replies: 8
Views: 2,934
Posted By cwhelan
If I end up with anything useful that offers...

If I end up with anything useful that offers something that these new packages don't I'll be sure to try to make that code available. :)
Forum: Bioinformatics 09-04-2012, 09:21 AM
Replies: 8
Views: 2,934
Posted By cwhelan
@Jluis I am not terribly familiar with...

@Jluis

I am not terribly familiar with methylkit; I was just reading about it because I've been writing a similar set of scripts for analysis of WGBS data and ran across it doing my research.
...
Forum: Bioinformatics 08-30-2012, 09:51 AM
Replies: 8
Views: 2,934
Posted By cwhelan
I can't speak to their accuracy yet but you might...

I can't speak to their accuracy yet but you might want to look into two new R packages for methylation data:

bsseq:

http://www.bioconductor.org/packages/2.11/bioc/html/bsseq.html

methylkit:...
Forum: Bioinformatics 07-31-2012, 09:19 AM
Replies: 2
Views: 1,485
Posted By cwhelan
Breakdancer reports all variants for which it has...

Breakdancer reports all variants for which it has enough support, in terms of then number of discordant read pairs, and does not call the genotype. Therefore, I think the output probably consists of...
Forum: Bioinformatics 02-28-2012, 01:47 PM
Replies: 6
Views: 3,570
Posted By cwhelan
In my experience I have not found...

In my experience I have not found realistic-looking or useable peaks in these types of data sets, unfortunately. I usually try to examine some of the peaks in a browser - you can tell pretty quickly...
Forum: Bioinformatics 02-27-2012, 11:48 AM
Replies: 6
Views: 3,570
Posted By cwhelan
This very insightful and helpful post by Anshul...

This very insightful and helpful post by Anshul Kundaje on the MACS mailing list has a really good theory involving the mappability of the genome for why you see this pattern in non-enriched ChIP-seq...
Forum: Bioinformatics 01-30-2012, 12:02 PM
Replies: 1
Views: 2,240
Posted By cwhelan
What I've been doing is to expand the calls into...

What I've been doing is to expand the calls into regions on each end and writing them out in BEDPE format:

chr1 start1 end1 chr2 start2 end2 strand1 strand2 name etc..

You can do this either by...
Forum: Bioinformatics 06-28-2011, 09:29 PM
Replies: 5
Views: 3,898
Posted By cwhelan
BreakDancer output question

I've been using BreakDancer for structural variation, and it works pretty well, but I'm a little bit confused by some of the output. My understanding is that BreadDancer categorizes translocations as...
Forum: Bioinformatics 06-08-2011, 09:49 AM
Replies: 7
Views: 3,394
Posted By cwhelan
You might also want to check out CloudBioLinux: ...

You might also want to check out CloudBioLinux:

http://cloudbiolinux.org/

which is an EC2 AMI that has many commonly used bioinformatics tools and data sets preinstalled. I've used it for small...
Forum: Bioinformatics 04-26-2011, 01:10 PM
Replies: 2
Views: 2,584
Posted By cwhelan
Another option is Condor: ...

Another option is Condor:

http://www.cs.wisc.edu/condor/
Forum: Bioinformatics 04-21-2011, 03:16 PM
Replies: 15
Views: 4,004
Posted By cwhelan
My thoughts on this are biased by my training in...

My thoughts on this are biased by my training in Agile development environments, but here's my two cents on one way to incentivize programmers to write documentation (if you'll stretch the definition...
Forum: Bioinformatics 03-16-2011, 11:03 AM
Replies: 649
Views: 183,126
Posted By cwhelan
bismark_to_SAM script for paired end data

Hi Oliver, Felix, and others,

I think there may be a small problem in the bismark_to_SAM_v2.pl script when converting paired end bismark output to SAM format. Specifically, I don't think it's...
Forum: Bioinformatics 02-03-2011, 10:47 AM
Replies: 649
Views: 183,126
Posted By cwhelan
Directional option and paired ends

I've been trying out Bismark and really like it so far.

I have a question about some of the results I'm seeing. I'm aligning paired-end Illumina BS reads against hg19, currently using Bismark...
Forum: Introductions 11-17-2010, 03:55 PM
Replies: 373
Views: 140,116
Posted By cwhelan
Hi Everyone, I'm a PhD student in computer...

Hi Everyone,

I'm a PhD student in computer science and computational biology in the Biomedical Engineering department at Oregon Health & Science University (OHSU). I'm currently working on trying...
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