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[mRNA-seq] 用unceqr软件通过RNA数据来验证DNA突变

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发表于 2016-12-8 09:15:42 | 显示全部楼层 |阅读模式
TCGA的例子;http://www.cell.com/cms/attachment/2035453106/2051015653/mmc1.pdf

In addition, we checked for the presence of somatic mutations in the RNAseq data for SMG mutations for samples with overlapping exome and RNAseq data by two methods. First, we counted sites powered by detection after adjusting for the read coverage in the RNAseq data for SMGs. We then used the percent of mutations validated by RNAseq as a proxy for the false positive rate of somatic mutation calls. Second, each tumor’s sequence mutations detected by DNA whole exome sequencing (DNA-WES) were interrogated for confirmation in their RNA sequencing (RNA-seq) using the tool UNCeqR (Wilkerson et al., 2014), as previously described (TCGA, 2012a, 2014b). DNA-WES mutation positions having a minimum of 1X and 5X RNA depth were evaluated for the presence of at least one read confirming the variant allele. Of mutation sites with at least 1X RNA depth, UNCeqR determined the sample-wise average mutation confirmation rate was 69%. Of mutation sites with at least 5X RNA depth, the samplewise average mutation confirmation rate was 80% (see panels A and B below). As expected, and similar to prior TCGA studies, the confirmation rate was greater among positions with

minimum 5X coverage, because there were more RNA reads and greater statistical power to confirm the variant allele than there was in the positions with minimum 1X coverage.

主要在TCGA的大文章里面有用到!
北卡开发的突变工具:http://nar.oxfordjournals.org/co ... nar.gku489.full.pdf
源码在github:https://github.com/mwilkers/unceqr
软件官网是:http://lbg.med.unc.edu/~mwilkers/unceqr_dist/
说明书没有,看github的介绍即可
The minimum requirements to run UNCeqR is a tumor sequencing alignment.
Additionally, there are a variety of data quality filtering options,
described in [1] and in the documentation provided within the software distribution.
For instance, mapping error alleles were calculated with the third party tool BlackOps tool.
The population and artifact allele site used in [1] is available with the software distribution.
Regenerating this allele list for different sequencing platforms is recommended.
The output of UNCeqR is a table of somatically mutated sites and associated information.
These somatic mutations can be annotated with predicted transcript and protein effects using third party tools, such as Annovar, as described in [1].




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