How to identify promoter sequences from plant NGS raw data

Question

[anikng]

Recently, I got genome sequencing data of a plant subspecies for which I HAVE WELL ANNOTATED REFERENCE SEQUENCE information. My objective is to comparative analysis of promoter regions of a few genes. How can I get the promoter region from NGS genome sequencing reads? Can anyone provide a correct method for that?

Thanks

Answer 1

[Devon Ryan]

If the well-annotated species and yours are highly related, then you'll likely have luck just aligning your reads against it and using it's reference annotation to call variants in promoter regions. Otherwise, you'd be better served by assembling your species and trying to align the contigs (you'd then find differences in the results). Since these are subspecies we're talking about, I assume the former possibility will work well and prove easier than the latter.

[anikng]

Thanks @ Devon Ryan.. I will look into it..Also i worry whether i can retrieve sequence rather than direct analysis to reference sequence.

[Devon Ryan]

Sorry, I can't parse your last sentence.

[anikng]

Sorry, what I mean is that in my case, I need to retrieve ~5kb upstream region of that gene (because I need that sequence for further MSA with other subspecies sequences I have). I am new to 'variant call in promoter region'. So, my impression is that using that method, I can identify the variation, but CANNOT fetch the sequence. @Devon Ryan

[Devon Ryan]

Ah, right, yes, calling the variants won't change the sequence. GATK has a tool that will convert a reference fasta file according to variants in a VCF file though.

[anikng]

Thanks a lot @Devon Ryan...I will look into it.