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Forum: Personalized Genomics 03-24-2015, 01:26 AM
Replies: 2
Views: 8,355
Posted By davetang
You can download the contigs of Craig Venter's...

You can download the contigs of Craig Venter's and James Watson's genome at ftp://ftp.ncbi.nih.gov/pub/TraceDB/Personal_Genomics/.
Forum: Bioinformatics 09-30-2014, 08:50 PM
Replies: 1
Views: 1,255
Posted By davetang
Hi Wilson, Repbase Update definitely has...

Hi Wilson,

Repbase Update definitely has consensus sequences for repeats in mouse, rat, and chicken.

Register a free account (http://www.girinst.org/server/RepBase/index.php) and download the...
Forum: Bioinformatics 07-29-2014, 11:06 PM
Replies: 1
Views: 4,365
Posted By davetang
I have exactly the same question and I haven't...

I have exactly the same question and I haven't been able to find more detailed information on the XT:A:M tag from BWA.

I created a simple example (on my blog at...
Forum: RNA Sequencing 07-07-2014, 05:55 PM
Replies: 4
Views: 2,816
Posted By davetang
Have a look at this paper for some perspective on...

Have a look at this paper for some perspective on CAGE versus RNA-Seq:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3975069/

Cheers,

Dave
Forum: RNA Sequencing 07-07-2014, 05:49 PM
Replies: 2
Views: 3,410
Posted By davetang
Hi Krys, have a look at this page and the...

Hi Krys,

have a look at this page and the references within: http://fantom.gsc.riken.jp/protocols/nanocage.html

Cheers,

Dave
Forum: Bioinformatics 07-07-2014, 04:15 PM
Replies: 1
Views: 931
Posted By davetang
Hello, the first three bases are the barcode...

Hello,

the first three bases are the barcode sequence, and the next 6 bases (CAGCAG) is the restriction site for EcoP15I, which is used in the CAGE protocol to cleave 27 nt upstream of the site....
Forum: Bioinformatics 03-10-2012, 06:50 PM
Replies: 7
Views: 15,549
Posted By davetang
Hello, As nilshomer suggested, use the Perl...

Hello,

As nilshomer suggested, use the Perl module use Bio::DB::Sam. I wrote some code which uses the module:

http://davetang.org/muse/2011/01/28/perl-and-sam/

The code is written by me, so...
Forum: Bioinformatics 01-19-2011, 04:29 PM
Replies: 7
Views: 15,549
Posted By davetang
Should have looked before I posted my question...

Should have looked before I posted my question but nevertheless this post could still be useful for someone else.

30M8D6M 27T2^ATGCATTT0G3T1

There is a 0 separating the 8 deletions and the...
Forum: Bioinformatics 01-19-2011, 04:13 PM
Replies: 7
Views: 15,549
Posted By davetang
SAM/BAM MD tag

Dear all,

I am writing a parser for the MD tag in SAM/BAM files because I couldn't find one. I am interested in tallying the alignment mismatches and the MD field contains the information I need....
Forum: Bioinformatics 08-24-2010, 04:01 AM
Replies: 6
Views: 10,402
Posted By davetang
Dear jlmlj, I used the parameters (bwa aln...

Dear jlmlj,

I used the parameters (bwa aln -n 7 -l 1000000) and I was able to align a read that had 5 mismatches to the reference. Running bwa on the default settings didn't report this alignment....
Forum: Introductions 07-20-2010, 06:03 PM
Replies: 1
Views: 1,541
Posted By davetang
Smile Hello from Japan

Hi everyone,

I've been mostly a lurker here but thought I'll introduce myself.

I've recently started my PhD project in transcriptomics and just starting to learn more about next generation...
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