What are the steps to follow to extract a promoter region starting from illumina 2000 fastq read

Question

[rus2dil]

What are the steps to follow to extract a promoter region starting from illumina 2000 fastq read? I am new to this and I want to use galaxy platform.

[Devon Ryan]

Am I correct in guessing that your sequencing reads are from an organism that lacks an annotation (or has a low quality annotation)? Otherwise, you don't need reads at all for this. Also, what sort of sequencing was used to produce the fastq files? One would hope that you used RNAseq and have a decent reference sequence. Otherwise, you're stuck with assembly followed by gene prediction, which is not the simplest procedure for someone new to things.

[rus2dil]

I have WGS unaligned raw reads. I need to extract the promoter region of a particular gene. I would like to know the steps from the scratch or a link to learn the process. Thanks

[Devon Ryan]

Provide answers to the questions posed. You have reads, we already knew that. Given the tags on your post you presumably think you need to assemble the genome, though whether that is actually the case or not remains to be seen.

Here's an unhelpful answer: (1) assemble the genome, (2) blast the sequence from a gene of interest against the assembled contigs, (3) get the promoter sequence given the resulting coordinates. I have no clue whether you can do this on galaxy, you can't always get what you want.

Answer 1

[Fidel]

[update] I overlooked the tags and didn't realise that the question was assembly specific.

It is not clear what you want, maybe you can be more specific. There are Illumina reads for many applications.

If you have some reads and want to see how they pile around TSS you need to align them to a reference genome and then you can try to plot the coverage around TSS. For this you can try deepTools in our Galaxy server.