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Hello folks,
Since I don't seem to have the privilege to post a new threads (even though it says so at the lower left corner in the page), please allow me to post a related question here.
In analyzing my human exome sequencing data (exome capture, Illumina high seq PE), I noticed the presence of split reads spanning the neighbouring exons as if they were RNA-seq data. This is repeatedly seen for the same junction in the same exome sequence data clearly as different reads not as PCR duplicates. In the same gene, there are reads spanning other neighbouring axons. My first thought was that they represented mRNA contamination in the DNA samples, but I was told that DNA was treated with RNnase. I guess then the other reason could be the presence of processed pseudogene, even though there is no annotated processed pseudogene for this particular gene. I guess one last possibility would be the existence of mutated genes with the introns deleted (perfectly at the intron/exon junction, which would be hard to image). I'd think that the first scenario is mostly like to be true due to incomplete elimination of mRNA, while the 2nd scenario could not be completely excluded, since polymorphic processed pseudogenes do exist. I'd like to see if anybody else have seen similar situations and whether you have any comments/suggestions.
Thank you very much!
Ping
Since I don't seem to have the privilege to post a new threads (even though it says so at the lower left corner in the page), please allow me to post a related question here.
In analyzing my human exome sequencing data (exome capture, Illumina high seq PE), I noticed the presence of split reads spanning the neighbouring exons as if they were RNA-seq data. This is repeatedly seen for the same junction in the same exome sequence data clearly as different reads not as PCR duplicates. In the same gene, there are reads spanning other neighbouring axons. My first thought was that they represented mRNA contamination in the DNA samples, but I was told that DNA was treated with RNnase. I guess then the other reason could be the presence of processed pseudogene, even though there is no annotated processed pseudogene for this particular gene. I guess one last possibility would be the existence of mutated genes with the introns deleted (perfectly at the intron/exon junction, which would be hard to image). I'd think that the first scenario is mostly like to be true due to incomplete elimination of mRNA, while the 2nd scenario could not be completely excluded, since polymorphic processed pseudogenes do exist. I'd like to see if anybody else have seen similar situations and whether you have any comments/suggestions.
Thank you very much!
Ping
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