accessing the gene on fastq data

Question

[Gülsüm]

Hi,

I have a whole genome data belong to a animal with fastq format. I need just some genes there to find the gene count. How can I do this?

[ATpoint]

Hi, please understand that with the given information one cannot help. What is "gene count"? Do you need gene expression data? What analysis are you doing?

[Darked89]

Do you have a genome assembly of some close species?

You can try to align your WGS FASTQs to such genome to get an idea how similar are these species at the genomic level.

Answer 1

[colindaven]

Normally assuming you have whole genome data

1. Take fastq data
2. Trim reads, eg with the tool fastp
3. Do a de novo assembly, eg with Soap2denovo or Abyss or another de novo assembler (assuming short reads, you did not say)
4. Run a gene finder like Maker, Helixer etc to do structural annotation
5. Get gene count

As you can see, it's a long process and you'll need to do a lot of google searching around this.