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

Question

[wu.zhiqiang.1020]

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

Answer 1

[Chirag Nepal]

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.

[wu.zhiqiang.1020]

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

[wu.zhiqiang.1020]

And I will read more about the program you introduced

ZQ

[Ashutosh Pandey]

Yes. It is Cufflinks BTW.