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.
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?
Yes, you can simulate reads from the fasta file, for example with
wgsimfrom the samtools package
Thank you very much for answering my post. I am afraid no one answers my question because it is too basic.