RNAseq: how can I extract the "expressed" reads regions from non-coding region?
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6.2 years ago

Hi All,

I get my RNA seq read (Single end) and we want to find the privious un-annotated trascripts among the genome. But how can I extract the boundary of these regions and the positions of them? I am a new to this area, so please give me some suggestion about it! Thanks!

ZQ

RNA-Seq small RNA • 1.4k views
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6.2 years ago
Chirag Nepal ★ 2.3k

1) Map raw reads to genome. [Use tools like, bwa/bowtie (small RNA reads), tophat ..etc]

2) To build transcripts, use cufflinks [edited the spelling]

3) Intersect the newly built transcript with ensembl and non-overlapping ones are what you are after.

There are many tutorial around, you need to search.

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Thanks Chirag Nepal.

you mean that the cifflinks could use the reads to build the all candidate transcripts (annotated and un-anntated). Is that right? 

ZQ

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And I will read more about the program you introduced

ZQ

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Yes. It is Cufflinks BTW.

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