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Old 12-15-2010, 03:00 AM   #1
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Default RNA-Seq: RNA-Seq Read Alignments with PALMapper.

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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]

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Old 02-27-2012, 12:57 AM   #2
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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!!
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