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Forum: General 10-31-2011, 12:36 PM
Replies: 3
Views: 1,691
Posted By What_Da_Seq
I believe if allele discrimination and phasing...

I believe if allele discrimination and phasing could be accomplish genome wide (we would know which region came from father/mother) it should be possible.
Forum: Pacific Biosciences 07-06-2011, 06:20 PM
Replies: 0
Views: 2,601
Posted By What_Da_Seq
Escherichia coli O104:H4 + 11 strains assemblies

Just in case the news thread missed this.

http://pacificbiosciences.com/sites/default/files/press_release_assets/Ecoli_data_release_announcement_Final_07062011.pdf

Anybody has any comments...
Forum: Academic/Non-Profit Jobs 06-03-2011, 11:40 AM
Replies: 15
Views: 6,295
Posted By What_Da_Seq
And do not get me started with post doc...

And do not get me started with post doc positions. Of course these positions are biology heavy and can be forgiven for lacking programming skills - that was the way in my case - my lab had a...
Forum: Academic/Non-Profit Jobs 06-03-2011, 11:28 AM
Replies: 15
Views: 6,295
Posted By What_Da_Seq
Of course I know my way around LINUX, how to...

Of course I know my way around LINUX, how to install and use the various packages described here (except cluster or cloud deployment), sequence editor (sed) and batch programming and how to break...
Forum: Academic/Non-Profit Jobs 06-03-2011, 08:42 AM
Replies: 15
Views: 6,295
Posted By What_Da_Seq
This is how the real world works. The people...

This is how the real world works. The people looking to hire bioinformatics professionals ALWAYS describe programmer jobs with a little bit of biology thrown in for good measure. That leaves us...
Forum: Sample Prep / Library Generation 11-18-2009, 11:22 AM
Replies: 27
Views: 11,540
Posted By What_Da_Seq
You are right IF damage occurs randomly. IF NOT...

You are right IF damage occurs randomly. IF NOT all the cool events happen in the 90% that you are loosing;)
Forum: Bioinformatics 11-18-2009, 06:09 AM
Replies: 5
Views: 3,022
Posted By What_Da_Seq
It is of course a statistical problem. What if...

It is of course a statistical problem. What if you adjust your read coverage (not your proportions) to a lower perhaps even consistent level - essentially taking read coverage out of the equation....
Forum: Bioinformatics 11-03-2009, 12:36 PM
Replies: 25
Views: 10,409
Posted By What_Da_Seq
Our 2 Xeon quad core, 32GB, 1.5TB Raid5 cost less...

Our 2 Xeon quad core, 32GB, 1.5TB Raid5 cost less than 3grand. You have to shop around for the memory and hard drives. And don't forget if you order a tower server the FANs are seriously loud.
Forum: Sample Prep / Library Generation 10-28-2009, 12:06 PM
Replies: 27
Views: 11,540
Posted By What_Da_Seq
How many single/di/trinucleotides are being...

How many single/di/trinucleotides are being generated by the fragmentation process - invisible to visualization and percent DNA lost in the fragment sizing step. Philip I get your line of inquiry and...
Forum: Bioinformatics 10-25-2009, 07:26 PM
Replies: 3
Views: 2,211
Posted By What_Da_Seq
Just ad a "rank#" column to the beginning and...

Just ad a "rank#" column to the beginning and label the next columns "chromosome" "start" "end" If you do not have more than 1.05 Mio rows you can doe it easily in Excel.
This is essentially a cod...
Forum: Bioinformatics 10-25-2009, 03:45 PM
Replies: 3
Views: 2,211
Posted By What_Da_Seq
cisgenome has a bunch of useful executables...

cisgenome has a bunch of useful executables (windows exe and LINUX binaries) and I suggest this one
refgene_getnearestgene
http://www.biostat.jhsph.edu/~hji/cisgenome/index_files/download.htm
Forum: Bioinformatics 09-29-2009, 12:57 PM
Replies: 14
Views: 10,645
Posted By What_Da_Seq
Also Dual 4 core Xeon (8 cores total). 32GB RAM,...

Also Dual 4 core Xeon (8 cores total). 32GB RAM, Redhat 5, Novoalign
Forum: Epigenetics 09-28-2009, 11:26 AM
Replies: 35
Views: 13,041
Posted By What_Da_Seq
BS mode of novoalign and from there Maq pilup and...

BS mode of novoalign and from there Maq pilup and then custom perl scripts.
Forum: Epigenetics 09-10-2009, 10:57 AM
Replies: 8
Views: 4,245
Posted By What_Da_Seq
I do not follow. Don't you want to do LESS...

I do not follow. Don't you want to do LESS shearing to get larger fragments?
Forum: Epigenetics 09-10-2009, 10:53 AM
Replies: 8
Views: 4,245
Posted By What_Da_Seq
Sorry no experience with de-novo assembly only...

Sorry no experience with de-novo assembly only reference based assembly.
Forum: Epigenetics 09-10-2009, 08:33 AM
Replies: 8
Views: 4,245
Posted By What_Da_Seq
why don't you treat your sequences as de-novo...

why don't you treat your sequences as de-novo assembly and try to align them with very very strict alignment parameters. This will hopefully result in many unique contigs that rely on small changes...
Forum: Bioinformatics 06-03-2009, 01:18 PM
Replies: 2
Views: 1,973
Posted By What_Da_Seq
Make sure you have the file in the same directory...

Make sure you have the file in the same directory as the novoindex executable or if not you have to use the proper path to the file. Hope that helps. I am indexing 3GB .fa files so it should not be a...
Forum: Bioinformatics 03-11-2009, 12:39 PM
Replies: 514
Views: 208,860
Posted By What_Da_Seq
Thanks Ben. I could not identify an option for...

Thanks Ben. I could not identify an option for "bowtie-build" that is geared towards maximum efficiency (not speed nor memory efficiency) in generating alignments (least amount of non-aligned reads)...
Forum: Bioinformatics 03-11-2009, 07:57 AM
Replies: 514
Views: 208,860
Posted By What_Da_Seq
How does Bowtie handle ambiguous bases in the refgenome

Does anybody have experience in preparing a Bowtie search index where certain bases have been modified with ambiguous bases like "Y" which stands for "C" or "T" and if so will these locations be...
Forum: Bioinformatics 02-20-2009, 07:28 PM
Replies: 13
Views: 5,338
Posted By What_Da_Seq
So far so good. it generates a huge amount of...

So far so good. it generates a huge amount of working files and I am still trying to figure out if I need the .mask and .int files for later steps or if I can just delete them after generating .bar...
Forum: Bioinformatics 02-14-2009, 11:47 AM
Replies: 13
Views: 5,338
Posted By What_Da_Seq
Turns out I do not have to build the database,...

Turns out I do not have to build the database, since the mm9 annotation file has it all (4GB). If you get the following error message "Couldn't open destination file!" you did not edit your .ini file.
Forum: Bioinformatics 02-13-2009, 01:54 PM
Replies: 13
Views: 5,338
Posted By What_Da_Seq
Trying to build the local genome database for mm9...

Trying to build the local genome database for mm9 in order to start annotating what I got from the analysis. The CisGenome MM9 annotation file seemed to be missing the refflat.txt files and all other...
Forum: Bioinformatics 02-12-2009, 12:02 PM
Replies: 66
Views: 28,049
Posted By What_Da_Seq
Sorry I did not make this clearer. Now that I...

Sorry I did not make this clearer. Now that I have done a couple analyses I can tell you that I am not getting any peaks using HMM and 2 samples when comparing (treatment > control) and only like 20...
Forum: Bioinformatics 02-09-2009, 12:31 PM
Replies: 66
Views: 28,049
Posted By What_Da_Seq
Any suggestions for using CisGenome for...

Any suggestions for using CisGenome for MeDIP-CHIP without input controls (only treated vs. notTreated)? I am still waiting for the normalization of my 63 .cel files to finish. I therefore have not...
Forum: Bioinformatics 02-09-2009, 12:23 PM
Replies: 13
Views: 5,338
Posted By What_Da_Seq
Just started using it for MeDIP-CHIP. Import is...

Just started using it for MeDIP-CHIP. Import is taking 5h so far (63 .cel files).
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