SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
Difference and similarity between Sanger,Illumina/Solexa and 454 sequencing data... edge Bioinformatics 0 09-07-2009 08:47 PM
Illumina solexa 75bp format problem anyone1985 Bioinformatics 5 08-31-2009 07:02 AM
Question about analysis problem for solexa sequencing of RNA profiles beckham423 Illumina/Solexa 0 08-24-2009 11:57 PM
PubMed: Swift: Primary Data Analysis for the Illumina Solexa Sequencing Platform. Newsbot! Literature Watch 0 06-25-2009 05:00 AM
Illumina/Solexa sequencing of human exons enriched with Nimblegen arrays ECO Illumina/Solexa 9 06-05-2009 01:58 PM

Reply
 
Thread Tools
Old 05-13-2010, 08:24 AM   #1
g781
Member
 
Location: Taiwan

Join Date: May 2010
Posts: 25
Default problem withe Illumina solexa sequencing

hi all,

I have a dataset with 4 columns, inculde chromosome, position, read count and direction (F/R), extracted from original Illumina solexa sequencing dataset, but the dataset have highly redanduncy. The dataset is about ~130Mb. However, the dataset reduced to ~30M dramatically when I removed the redanduncy datas.

Whether the original dataset is wrong or nothing?
g781 is offline   Reply With Quote
Old 05-13-2010, 09:16 AM   #2
NextGenSeq
Senior Member
 
Location: USA

Join Date: Apr 2009
Posts: 482
Default

You want high coverage (which is what I think you mean by redundancy). Typically people shoot for at least 20x coverage for SNP and indel detection.
NextGenSeq is offline   Reply With Quote
Old 05-13-2010, 10:15 AM   #3
g781
Member
 
Location: Taiwan

Join Date: May 2010
Posts: 25
Default

The dataset is used to map the distrubution of nucleosomes in yeast genome. could I ask you whether the highly coverage dataset is able to map nucleosome distrubution.

I have used a template filtering program, published from Genome Res. 2010 Jan;20(1):90-100, to map the distrubution of nucleosomes. My condition is normal as wild-type, so typically the result should be the same with figrue 3D (yellow). However, the result is different the figure 3D (see yellow). Therefor, I doubt whether the highly coverage dataset is the cause of making results inconsistent.

My result is following:
http://140.116.247.56/g781/tss.jpg

Last edited by g781; 05-13-2010 at 10:20 AM.
g781 is offline   Reply With Quote
Old 05-18-2010, 10:05 AM   #4
Nik
Member
 
Location: London

Join Date: May 2009
Posts: 14
Default

I'm not sure what you really mean but I've had something similar and this was due to duplications.
Nik is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:15 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO