How to extract CDS from WGS data in rice?

Question

[ChanderKant (CK) Chaudhary]

Dear All,

I would like to confirm that I am extracting the CDS from WGS data correctly. Below are the steps I followed:

1. Generated a consensus FASTA sequence from the BAM file.
2. Retrieved the target gene sequence using its genomic coordinates from RAP-DB.
3. Performed a multiple sequence alignment (MSA) between the extracted genomic  DNA (gDNA) sequence and the known CDS of the gene.
4. Identified the matching region and extracted it.
5. I am considering this extracted region as the putative CDS for the specific rice genotype.

Please let me know if any corrections or improvements are needed.

Thank you for your time.

Best,

CK

[Mark]

I would annotate the consensus then extract the CDS. I am not sure what tool is used for plants.

[ChanderKant (CK) Chaudhary]

Hi Mark,

Thank you. I can use EDTA for annotation. What tool do you use for your system?

Thank you for your time.

Best,

CK

[Mark]

I work on viruses/bacteria, completely different field.