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accessing the gene on fastq data

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?

rna-seq sra
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updated by Darked89 Darked89 • written by Gülsüm • Gülsüm

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?

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written by ATpoint ATpoint

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.

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written by Darked89 Darked89

1 answer

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.

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written by colindaven colindaven

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