What are the steps to extract a particular sequence from a WGS raw read

Question

[rus2dil]

I am new to bioinformatics and recently I started a research project to compare promoters of a particular gene (not decided yet). I have several raw reads of WGS deposited in ENA site. How should I use these raw reads to extract a particular region? For example, sequence of the rice LEAFY gene.

Answer 1

[Ashutosh Pandey]

Download the data and align it against the rice reference genome. Then use the coordinates of the gene you are looking for and extract those sequences from the BAM file using samtools.

[rus2dil]

Thank you very much Ashutosh Pandey. I think using galaxy platform I can do this? Right?

[Ram]

Yes, upload FASTQ, align to ref genome. Then use SAM manipulation tools and a BED file to extract the region.

[rus2dil]

Thank you RamRS. Should this BED file only contain the sequence of interest? If so, how to create it from FASTQ or FATSA file. Because I have the FASTA file of the gene of interest downloaded from the reference genome.

[Ram]

BED is for co-ordinates of your gene of interest. Use UCSC genome browser and beware the index differences in tools (Check out this post for more details)