Does anyone think the peaks in non-coding region could be some bias or random events, rather than some potential ncRNA? BTW, the organism is prokaryotic. Thanks!
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Google "pervasive transcription."
I think there is far more "noise" in transcription than people give credit too. Of course there is far from any consensus on the matter.
Short-read RNA sequencing in mouse and human tissues shows that most transcripts are encoded within or nearby known genes and that most of the genome is not transcribed.
Despite recent controversies, the evidence that the majority of the human genome is transcribed into RNA remains strong.
RNA sequencing,Human genomics,Introns,Small nucleolar RNA,Long non-coding RNA,Messenger RNA,Expressed sequence tags,RNA analysis
RNA Polymerase II can have a lot of false starts, producing transcripts that may or may not be functional:
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It is extremely unlikely that the sequencer randomly comes up with a sequence that actually maps to your genome unless this sequence was actually in the sample. So, this is definitely not a technical proble -- the non-coding sequences were in your sample, and so they were also transcribed by your cells. (Alternatively, it could be genomic DNA that sneaked into your RNA sample.)
Why do you think that it makes a difference that your sample is prokaryotic?
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Originally posted by Simon Anders View PostIt is extremely unlikely that the sequencer randomly comes up with a sequence that actually maps to your genome unless this sequence was actually in the sample. So, this is definitely not a technical proble -- the non-coding sequences were in your sample, and so they were also transcribed by your cells. (Alternatively, it could be genomic DNA that sneaked into your RNA sample.)
Why do you think that it makes a difference that your sample is prokaryotic?
Like you said, the small peaks in the intergenic regions could be genomic DNA. Or it could also be novel ncRNAs with low expression level. If it's the previous situation, I can consider it as a noise in my background, and include it into my negative set for training; but if it's the latter case, I should definitely exclude the peak region to train my negative set.
BTW, when I mapped the reads to the reference genome, I only kept the uniquely mapped reads with tolerance of 3 mismatches. The read length is 100nt. Therefore, I don't think the small peaks are mapping artifacts...
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Originally posted by chadn737 View PostGoogle "pervasive transcription."
I think there is far more "noise" in transcription than people give credit too. Of course there is far from any consensus on the matter.
Short-read RNA sequencing in mouse and human tissues shows that most transcripts are encoded within or nearby known genes and that most of the genome is not transcribed.
Despite recent controversies, the evidence that the majority of the human genome is transcribed into RNA remains strong.
RNA sequencing,Human genomics,Introns,Small nucleolar RNA,Long non-coding RNA,Messenger RNA,Expressed sequence tags,RNA analysis
RNA Polymerase II can have a lot of false starts, producing transcripts that may or may not be functional:
http://www.nature.com/nsmb/journal/v...b0207-103.html
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