Retrieval of Promoter sequence from RNASeq reads

[anikng]

Hi members,

My intention is to get the promoter sequence of a a specific gene from paired end illumina RNASeq reads.

Now I aligned those sequences to the reference chromosome using Tophat and got the BAM file. At this point, I dont know how to accurately retrieve the promoter sequence of that gene from BAM file.

So, If anyone can suggest me the best method,it would be very helpful for me.

Thank you in advance...

anikng,
ROK

[dpryan]

There are specific protocols designed to more accurately denote the bounds of transcripts, you'd be wise to use one of them if getting this right is vitally important (or just do 5' RACE and then you'll know the actual gene bounds).

In general, you want to look at the extrema of where the reads map. If the gene of interest is on the + strand, then the 5' most reads should approximately mark its 5'-most extent. The promoter is what precedes it then. The opposite is then true for genes on the - strand.

Note that typical RNAseq bias and multiple transcript start sites will make this somewhat inaccurate, but presumably that's OK...otherwise you'd use a different method.

[anikng]

Hi dpryan,

Thanks for the information. But it would be more helpful for me if u can suggest any specific tools or method (for which i can get more on google search).

anikng