SEQanswers

Go Back   SEQanswers > Literature Watch



Similar Threads
Thread Thread Starter Forum Replies Last Post
PubMed: Error correction of next-generation sequencing data and reliable estimation o Newsbot! Literature Watch 0 07-31-2010 08:56 AM
PubMed: Structural shifts of gut microbiota as surrogate endpoints for monitoring hos Newsbot! Literature Watch 0 07-16-2010 02:00 AM
PubMed: Assembly algorithms for next-generation sequencing data. Newsbot! Literature Watch 1 03-10-2010 09:06 AM
Paper: Substantial biases in ultra-short read data sets from HTP DNA sequencing ECO Illumina/Solexa 0 08-02-2008 05:16 PM
PubMed: Substantial biases in ultra-short read data sets from high-throughput DNA seq Newsbot! Literature Watch 0 07-29-2008 05:10 AM

Reply
 
Thread Tools
Old 04-26-2011, 02:10 AM   #1
Newsbot!
RSS Posting Maniac
 

Join Date: Feb 2008
Posts: 1,439
Default PubMed: SAMStat: monitoring biases in next generation sequencing data.

Syndicated from PubMed RSS Feeds

SAMStat: monitoring biases in next generation sequencing data.

Bioinformatics. 2011 Jan 1;27(1):130-1

Authors: Lassmann T, Hayashizaki Y, Daub CO

The sequence alignment/map format (SAM) is a commonly used format to store the alignments between millions of short reads and a reference genome. Often certain positions within the reads are inherently more likely to contain errors due to the protocols used to prepare the samples. Such biases can have adverse effects on both mapping rate and accuracy. To understand the relationship between potential protocol biases and poor mapping we wrote SAMstat, a simple C program plotting nucleotide overrepresentation and other statistics in mapped and unmapped reads in a concise html page. Collecting such statistics also makes it easy to highlight problems in the data processing and enables non-experts to track data quality over time.

PMID: 21088025 [PubMed - indexed for MEDLINE]



More...
Newsbot! 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 06:06 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO