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Old 08-16-2016, 07:23 PM   #1
lingling huang
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Location: changsha

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Default How to find polycistronic transcripts in eukaryotes genomes

Hi,there.
I have got long, high-quality, consensus transcripts sequences, and I want to see weather there are polycistronic transcripts in my PacBia data.I have extracted the long open reading frames and predicted the likely coding regions by using TransDecoder.Then, I don't know how to calculate how many orfs in transcripts and filter for polycistronic candidates and get support from genome-based annotation. Any hints or links would be appreciated.Thank you!
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Old 08-17-2016, 05:28 AM   #2
Macspider
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I'm not an expert on PacBio data, but I think you can hardly determine if they are polycistronic or not without a reference genome.
With coding region predictors you can only guess which parts of the sequence of your transcripts are translated and which not, but this makes sense only if you have primary transcripts sequenced and not mRNAs. In the latter case, you won't have any intron in your sequence and thus you will predict, for each transcript, a 5'UTR + a CDS + a 3'UTR.

If you have time to spend on this, you will definitely benefit to map the reads to a reference.

Are your PacBio data full length transcripts?
Do you have a reference to align to?
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Old 08-17-2016, 04:48 PM   #3
lingling huang
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Quote:
Originally Posted by Macspider View Post
I'm not an expert on PacBio data, but I think you can hardly determine if they are polycistronic or not without a reference genome.
With coding region predictors you can only guess which parts of the sequence of your transcripts are translated and which not, but this makes sense only if you have primary transcripts sequenced and not mRNAs. In the latter case, you won't have any intron in your sequence and thus you will predict, for each transcript, a 5'UTR + a CDS + a 3'UTR.

If you have time to spend on this, you will definitely benefit to map the reads to a reference.

Are your PacBio data full length transcripts?
Do you have a reference to align to?
Yes, my data are full-length non-chimeric transcripts and have a human reference. Therefore, I want to try to align them to human genome.
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