How to align and visualize data with .fasta and .gff3 files in IGV?

Question

[Phuc]

Hi everyone,

I have an issue in aligning and visualizing my data in IGV. As I read in manual of IGV, to align and visualize data, I need to to prepare .BAM/.SAM or other input format suitable with IGV. However, I only have .fasta file that contains whole genome and .gff3 gene annotation file of my samples, which can generate the .genome format for reference only.

Can someone suggest me some tools or scripts to combine .fasta genome and .gff3 gene annotation file then convert it to .bam file?

P/s: I'm new in bioinformatic and I need to use IGV for my study.

Answer 1

[Carambakaracho]

From your question it's pretty clear you're very new in bioinformatics. All I can offer is some buzzwords, and then there's a bit of reading required on your side.

What you have is the reference genome (fasta sequence) and its annotation (gff). You'll need some sequencing data, which typically come in compressed fastq format (like fastq.gz) file ending, which you can align to your reference genome to create a bam file. Popular short read aligners include bwa-mem and bowtie2, however, there's many more. These aligners create sam, or it's binary bam format. You can convert between both formats using samtools.

[Phuc]

Thank you for your help Carambakaracho . I will try to look back my data whether I have the fastq format file or not. In case if I don't have the fastq format file, can I make a new one from fasta format file?

[Carambakaracho]

Yes, you can simulate reads from the fasta file, for example with wgsim from the samtools package

[Phuc]

Thank you very much for answering my post. I am afraid no one answers my question because it is too basic.