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Search: Posts Made By: Michael.James.Clark
Forum: Bioinformatics 02-18-2014, 01:37 PM
Replies: 8
Views: 93,144
Let me just say that I think this is a very...

Let me just say that I think this is a very important project and I'm excited that it's getting off the ground. Somatic calling needs to undergo substantial advancement, so this project will be vital...
Forum: Bioinformatics 02-07-2014, 09:34 AM
Replies: 2
Views: 2,102
Do you think this an appropriate aligner to use...

Do you think this an appropriate aligner to use to fully take advantage of the new reference genome given its structure?

It seems incorrect to take a tool optimized for the linear GRCh37, apply it...
Forum: Bioinformatics 07-13-2012, 10:29 PM
Replies: 6
Views: 6,649
Indeed it would be!

Indeed it would be!
Forum: Bioinformatics 07-09-2012, 09:32 AM
Replies: 8
Views: 9,743
Related to the topic of this thread: If we...

Related to the topic of this thread:

If we are re-aligning paired data from a previously aligned bam file (because I had a bam file returned to me from a vendor rather than fastq files), what is...
Forum: General 06-14-2012, 10:48 PM
Replies: 2
Views: 1,010
Great question. ANNOVAR has limited ability to at...

Great question. ANNOVAR has limited ability to at least annotate exon-intron boundaries by defining X number of bases at the exon-intron boundary as "splicing".

This is fairly inaccurate, but...
Forum: Bioinformatics 06-05-2012, 11:12 AM
Replies: 10
Views: 5,288
RE: ANNOVAR dbSNP annotation taking a long time. ...

RE: ANNOVAR dbSNP annotation taking a long time.

Try using "--batchsize 50m" in your annotate_variation.pl command.

Dropped my run time on dbSNP135 from 20 hours to 20 minutes on 7.5M variants.
Forum: Bioinformatics 12-14-2011, 02:24 PM
Replies: 4
Views: 2,636
Basically sequences not present in the reference...

Basically sequences not present in the reference genome, but present in humans and that should be aligned against for the most accurate/sensitive results.

Thanks for that link, Heng Li. I feel...
Forum: Bioinformatics 12-13-2011, 02:06 PM
Replies: 4
Views: 2,636
Alignment to b37 with decoy sequences

Hi all,

I've heard from 1kG that alignment to b37 with decoy sequences is superior to without decoy sequences. Obviously the decoy is there to improve our results, but I'm just wondering if others...
Forum: Bioinformatics 12-12-2011, 01:01 PM
Replies: 45
Views: 18,121
I don't think PennCNV is a SV algorithm, is it? I...

I don't think PennCNV is a SV algorithm, is it? I mean, CNVs are technically SVs, but it's a CNV program isn't it? Or does it call things like translocations and indels?

GASV I haven't used, so I...
Forum: Bioinformatics 12-12-2011, 12:33 PM
Replies: 45
Views: 18,121
Hi Mark, Breakway will call five types of...

Hi Mark,

Breakway will call five types of SVs:
Deletions
Insertions
Interchromosomal Translocations
Intrachromosomal Translocations
Inversions

Copy changes are typically going to fall...
Forum: Bioinformatics 10-17-2011, 02:47 PM
Replies: 45
Views: 18,121
Actually, Breakway doesn't have a 4-read limit....

Actually, Breakway doesn't have a 4-read limit. It can report an event based on as little as one read if you tell it to.
Forum: Bioinformatics 10-16-2011, 11:07 AM
Replies: 45
Views: 18,121
SNP detection is another type of analysis all...

SNP detection is another type of analysis all together, really. I'm not a big believer in "reinventing the wheel", and I feel both GATK and samtools do a fantastic job at SNP detection.

My...
Forum: Bioinformatics 10-16-2011, 03:09 AM
Replies: 45
Views: 18,121
The paper is "U87MG Decoded", PLoS Genetics, Jan...

The paper is "U87MG Decoded", PLoS Genetics, Jan 2010

As I said, Breakway is stable. It hasn't been updated in a while because it doesn't require any updating. I'm not sure what you mean by a...
Forum: Bioinformatics 10-15-2011, 06:07 PM
Replies: 45
Views: 18,121
Breakway should work as well now as it did the...

Breakway should work as well now as it did the last time I updated it. :) As far as I know, it's bug free and works as described.


As far as I know, yes. I do not think samtools has had any of...
Forum: Bioinformatics 10-13-2011, 01:46 PM
Replies: 10
Views: 5,529
Oh, well in that case, I know exactly which tool...

Oh, well in that case, I know exactly which tool you could use: An undergrad. ;)
Forum: Bioinformatics 10-13-2011, 01:30 PM
Replies: 138
Views: 60,012
Annovar can annotate with SIFT and Polyphen now.

Annovar can annotate with SIFT and Polyphen now.
Forum: Bioinformatics 10-13-2011, 01:29 PM
Replies: 10
Views: 5,529
I just throw them in FinchTV and look with my...

I just throw them in FinchTV and look with my eyes. I guess that might be a lot of work if you're doing more than a handful of samples, though.
Forum: Literature Watch 10-13-2011, 10:52 AM
Replies: 5
Views: 9,050
Updated the first post to include additional...

Updated the first post to include additional papers.
Forum: Bioinformatics 10-13-2011, 10:21 AM
Replies: 138
Views: 60,012
Very cool! I was planning to put together a...

Very cool! I was planning to put together a little Google Site going through how I analyze exome-seq that's very similar to this. Now I'm not sure I should bother! :)
Forum: Literature Watch 10-09-2011, 01:59 AM
Replies: 5
Views: 9,050
Thanks, that should say "101-bp".

Thanks, that should say "101-bp".
Forum: General 10-08-2011, 12:01 AM
Replies: 6
Views: 1,875
Fix the path to your tmpDir. It's wrong if you're...

Fix the path to your tmpDir. It's wrong if you're getting that error.

Just did this today with "-T tmp/" and it worked fine. :)
Forum: Site Feedback/Suggestions 10-07-2011, 11:58 PM
Replies: 430
Views: 55,570
Thanks for your hard work, Marco. :)

Thanks for your hard work, Marco. :)
Forum: Literature Watch 10-07-2011, 01:53 PM
Replies: 5
Views: 9,050
Exome-sequencing platform comparison papers

Performance comparison of exome DNA sequencing technologies (http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.1975.html)

Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, Euskirchen G,...
Forum: Site Feedback/Suggestions 10-07-2011, 01:42 PM
Replies: 430
Views: 55,570
I think this is fantastic. I added a few things...

I think this is fantastic. I added a few things and made a few cosmetic edits. Great job, and please let me help out.

I especially wanted to add reference to this paper...
Forum: Sample Prep / Library Generation 10-05-2011, 11:14 AM
Replies: 10
Views: 3,877
You are not alone. This is an issue with the...

You are not alone. This is an issue with the SureSelect platform. I believe the best solution we've had is the PCR plate/tubes with strip caps and just a lot of care when opening tubes in case liquid...
Showing results 1 to 25 of 214

 


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