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Old 12-27-2011, 03:00 AM   #1
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Default RNA-Seq: RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

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RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

Nucleic Acids Res. 2011 Dec 22;

Authors: Chen LY, Wei KC, Huang AC, Wang K, Huang CY, Yi D, Tang CY, Galas DJ, Hood LE

Abstract
Next-generation sequencing (NGS) technologies-based transcriptomic profiling method often called RNA-seq has been widely used to study global gene expression, alternative exon usage, new exon discovery, novel transcriptional isoforms and genomic sequence variations. However, this technique also poses many biological and informatics challenges to extracting meaningful biological information. The RNA-seq data analysis is built on the foundation of high quality initial genome localization and alignment information for RNA-seq sequences. Toward this goal, we have developed RNASEQR to accurately and effectively map millions of RNA-seq sequences. We have systematically compared RNASEQR with four of the most widely used tools using a simulated data set created from the Consensus CDS project and two experimental RNA-seq data sets generated from a human glioblastoma patient. Our results showed that RNASEQR yields more accurate estimates for gene expression, complete gene structures and new transcript isoforms, as well as more accurate detection of single nucleotide variants (SNVs). RNASEQR analyzes raw data from RNA-seq experiments effectively and outputs results in a manner that is compatible with a wide variety of specialized downstream analyses on desktop computers.


PMID: 22199257 [PubMed - as supplied by publisher]



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Old 02-07-2012, 07:40 PM   #2
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Default RNASEQR v1.0.2, Feb 7 2012

RNASEQR (version 1.0.2.) is released. Please read the manual to find out the latest changes. A quick change log is attached here.

Version 1.0.2
1. add support to the gene annotation and gene reference sequences from UCSC Table Browser download.
2. add filter_alternative_loci_ENS.pl and filter_alternative_loci_UCSC_BED.pl scripts to fix an issue due to the transcriptomic index when running paired-end library.
3. add create_map_and_tables.pl script to fix hard-coded chromosome information stored in the map_and_tables.py.

Version 1.0.1
1. add convert_CASAVA1.8_headers.pl to fix an issue caused by CASAVA 1.8 header when running paired-end libraries.
2. add convert_CASAVA_export.py to convert CASAVA export text file to FASTQ format.
3. add convert_RNASEQRSAM_to_CufflinkSAM.py to support the Cufflinks analysis.

Last edited by chenyyl; 02-08-2012 at 10:31 AM.
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