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Old 03-16-2012, 03:39 AM   #1
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Location: Ireland

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Default Review paper about quality issues in RNA-seq data??

Hi everyone,

I'm wondering if there exists a paper discussing things like sequence quality degradation, sequence duplication, library contamination, etc. and approaches currently used to address these issues in NGS/RNA-seq?

I haven't been able to find anything decent but I'd imagine there must be something like this out there?

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Old 03-27-2012, 06:26 AM   #2
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Here is an "old" one:
Comprehensive comparative analysis of strand-specific RNA sequencing methods
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Old 03-27-2012, 07:38 AM   #3
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Here is a few useful papers:

Nucleic Acids Res. 2012 Feb 9;
Summarizing and correcting the GC content bias in high-throughput sequencing.

Biotechniques. 2012 Feb;52(2):87-94. doi: 10.2144/000113809.
Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries.

Nucleic Acids Res. 2011 Aug;39(15):e103. Epub 2011 Jun 6.
Systematic bias in high-throughput sequencing data and its correction by BEADS.

Nucleic Acids Res. 2010 July; 38(12): e131.
Biases in Illumina transcriptome sequencing caused by random hexamer priming
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