Paper(S) Discussing Issues In Quality Assessment Of Ngs Data

Question

[Paul]

Hi,

I'm wondering if anyone is aware of any good review papers outlining the main issues in quality assessment of NGS data, particularly Illumina RNA-seq data if at all possible.

I've used FastQC for quality assessment, but it isn't published and I'm wondering if there are other papers which back it up.

Thanks!

Answer 1

[Sean Davis]

Take a look at the picard CollectRnaSeqMetrics tool. I'm not suggesting that it is the only tool, but it does give some useful statistics and will certainly highlight samples that are outliers after alignment.

Answer 2

[Ian]

You might find this BioStar link of use.

My own suggestion of htSeqTools and HOMER is still for general NGS datasets.