Hello all, I am working with both DNA exome sequencing and RNAseq data. The samples are not directly matched, but they are of the same disease, and therefor I was hoping to use the RNAseq to check for the variants detected in DNA sequencing and visa versa. The problem is the RNAseq data is so noisy that there are far too many variants ( most of which are systematics) to do this analysis. I have thus far filtered using dbSNP, depth and frequency, and filtering out things detected in a separate panel of RNAseq normal cells that I have. Does anyone have any advice on how to trim the list down further? Perhaps some papers or examples of other groups that have done something similar? Any advice would be greatly appreciated! Thanks for your time
Question: Ways To Filter Noise From Rnaseq Data
5.6 years ago by
Wayne • 950
Wayne • 950 wrote:
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5.5 years ago by
JC ♦ 6.7k
JC ♦ 6.7k wrote:
Calling variants in RNAseq is noisy but you can improve your calling in several ways:
- First be sure that you library is good, remove low quality reads before mapping, also check if you need trimming, Istvan already mentioned some tools for that.
- Use a good mapper, Malachi pointed some tools.
- Call your variants with a tool which can perform realignment, such as GATK or samtools, use higher quality filters.
- Besides dbSNP, you can verify if the variant is known in other databases such as Kaviar.
5.5 years ago by
Istvan Albert ♦♦ 77k
University Park, USA
Istvan Albert ♦♦ 77k wrote:
Here is a post on different RNA-seq quality filtering options RSeqQC and RNA-SeqQC - quality control software for RNA-Seq data
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