How to identify gene list present in Whole genome sequencing data?

Question

[mail2steff]

Dear All,

I am new to Whole genome sequencing analysis. I have two sample fastq files. I have run fastqc and bowtie2 using reference genome (papaya). I got the sam file. Now How to computationally identify the list of genes and their locations present in my file. I need all the gene list. So I can find GO annotations

[Neel]

Hi, i have some problem, i mean i want to extract gene list from 200 GTF file E.coli sequences but the problem is how can i separate a gene which are not annotated or present in gff file with their gene name.

Thank you

Answer 1

[JC]

If you are using a reference genome, there probably a gene annotation file (GTF, GFF3). Search in Phytozome for the annotations and try to see gene coverage, for that you can use Bamtools or similar tools.

[mail2steff]

I downloaded papaya reference genome in fasta file from NCBI and did alignment using Bowtie2

[mail2steff]

##species Carica papaya
contig_23646    phytozomev11    gene    5096    5506    .   -   .   ID=evm.TU.contig_23646;Name=evm.TU.contig_23646
contig_23646    phytozomev11    mRNA    5096    5506    .   -   .   ID=PAC:16429340;Name=evm.TU.contig_23646.3;pacid=16429340;longest=1;Parent=evm.TU.contig_23646
contig_23646    phytozomev11    CDS 5096    5506    .   -   0   ID=PAC:16429340.CDS.1;Parent=PAC:16429340;pacid=16429340

I downloaded the gff3 file from Phytozome. But in that , there is no gene name in it.

[JC]

Cpapaya_113_ASGPBv0.4.annotation_info.txt file contains the annotation and mapping to Arabidopsis