SEQanswers

Go Back   SEQanswers > Literature Watch



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-Seq: Characterizing short read sequencing for gene discovery and RNA-Seq analysis Newsbot! Literature Watch 0 01-17-2012 06:50 AM
RNA-Seq: Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Newsbot! Literature Watch 3 07-31-2011 08:08 PM
RNA-Seq: SAMMate: a GUI tool for processing short read alignments in SAM/BAM format. Newsbot! Literature Watch 0 01-15-2011 03:50 AM
RNA-Seq: Modeling non-uniformity in short-read rates in RNA-Seq data. Newsbot! Literature Watch 2 06-29-2010 02:47 PM

Reply
 
Thread Tools
Old 12-15-2010, 03:00 AM   #1
Newsbot!
RSS Posting Maniac
 

Join Date: Feb 2008
Posts: 1,443
Default RNA-Seq: RNA-Seq Read Alignments with PALMapper.

Syndicated from PubMed RSS Feeds

RNA-Seq Read Alignments with PALMapper.

Curr Protoc Bioinformatics. 2010 Dec;Chapter 11:Unit11.6

Authors: Jean G, Kahles A, Sreedharan VT, Bona FD, Rätsch G

Next-generation sequencing technologies have revolutionized genome and transcriptome sequencing. RNA-Seq experiments are able to generate huge amounts of transcriptome sequence reads at a fraction of the cost of Sanger sequencing. Reads produced by these technologies are relatively short and error prone. To utilize such reads for transcriptome reconstruction and gene-structure identification, one needs to be able to accurately align the sequence reads over intron boundaries. In this unit, we describe PALMapper, a fast and easy-to-use tool that is designed to accurately compute both unspliced and spliced alignments for millions of RNA-Seq reads. It combines the efficient read mapper GenomeMapper with the spliced aligner QPALMA, which exploits read-quality information and predictions of splice sites to improve the alignment accuracy. The PALMapper package is available as a command-line tool running on Unix or Mac OS X systems or through a Web interface based on Galaxy tools.Curr. Protoc. Bioinform. 32:11.6.1-11.6.37. © 2010 by John Wiley & Sons, Inc.

PMID: 21154708 [PubMed - as supplied by publisher]



More...
Newsbot! is offline   Reply With Quote
Old 02-27-2012, 12:57 AM   #2
zun
Member
 
Location: Japan

Join Date: Oct 2010
Posts: 26
Default

Hi there,

I don't know if somebody would see my reply to this thread, but let me ask one question.

Can PALmapper treat paired-end reads ? I can see there are options for left/right reads(-q1,-q2), so run PALmapper with paired-end reads, but the result was not as I expected...inside the samfile, there were no CIGAR "=" which means the read has mate pair...

Does anyone know about paired-end reads treated by PALmapper??

I appreciate any help in advance!!
zun 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 05:37 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO