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Old 11-18-2012, 01:02 PM   #1
figo1019
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Default PolyA removal from RNA seq Illumina reads

Hi All,

I have paired end RNA seq Illumina reads. Do i need to remove the PolyA from the reads ( is it required) in the preprocessing step of Reads. What are the software to do it? .I am little bit confused on this can any one tell me.Is it require to remove the PolyA from your RNA seq Illumina reads ?

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Old 11-18-2012, 03:06 PM   #2
schlesin
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Depends on what you want to do with the reads. Some RNA-seq mappers can handle trimming directly. See e.g. http://bioinformatics.oxfordjournals...s.bts635.short
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Old 11-18-2012, 06:06 PM   #3
JackieBadger
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From the MIRA assembler documentation

"9.2.1. Poly-A tails in EST data

Poly-A tails are part of the mRNA and therefore also part of sequenced data. They can occur as poly-A or poly-T, depending from which direction and which part of the mRNA was sequenced. Having poly-A/T tails in the data is a something of a double edged sword. More specifically., if the 3' poly-A tail is kept unmasked in the data, transcripts having this tail will very probably not align with similar transcripts from different splice variants (which is basically good). On the other hand, homopolymers (multiple consecutive bases of the same type) like poly-As are features that are pretty difficult to get correct with today's sequencing technologies, be it Sanger, Solexa or, with even more problems problems, 454. So slight errors in the poly-A tail could lead to wrongly assigned splice sites ... and wrongly split contigs.

This is the reason why many people cut off the poly-A tails. Which in turn may lead to transcripts from different splice variants being assembled together.

Either way, it's not pretty. "
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