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coverage is around 10X with unique and filtered reads.
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Hi there,
I am confused with my RNASeq analysis result. After mapping the reads to Human reference using TopHat, 62% is mapped to the intronic or intergeneric region.
Here is short summary about my experiment:
1. Extract total RNA using Qiagen RNAmini kit
2. Prepare library using Illumina TrueSeq protocol
I am wondering maybe this is due to the high amount of premature mRNA. How do you think? Does anyone have the simillar experience? Any comment is welcome.
Thank you so much for your attention,
LahomanComment
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What portion of the reads mapped to intergenic regions? Were those regions close to or distant from genes? Perhaps the DNA digestion step in your RNA extraction failed and you actually sequenced a mix of DNA and mRNA. Check the genomic regions where the reads map to for poly-A runs.Comment
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