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

Hi All,

I get my RNA seq read (Single end) and we want to find the previous un-annotated transcripts 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
• 2,821 views • link
updated by Ram Ram • written by wu.zhiqiang.1020 • wu.zhiqiang.1020

1 answer

  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.

• 0 views • link
updated by Ram Ram • written by Chirag Nepal Chirag Nepal

Thanks Chirag Nepal.

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

ZQ

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updated by Ram Ram • written by wu.zhiqiang.1020 • wu.zhiqiang.1020

And I will read more about the program you introduced

ZQ

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updated by Ram Ram • written by wu.zhiqiang.1020 • wu.zhiqiang.1020

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