I'm a new bio PhD student, just starting in the lab. I'm trying to view 3 different versions of the Eucalyptus genome so I can compare what they all have for a particular gene because it appears there may be an inconsistency.
I tried running IGV and received a message saying the files needed to be sorted before I could load them. To sort them, I first tried IGVtools, but can't get it to work with my Java... Just downgraded so I could get Figtree to work, then re-upgraded again and I still get a message telling me to update, so IGVtools won't work for me.
I'm trying to use Samtools instead. I type: samtools sort library/eggenome/1.0genes.gff3 -o 1.0gene.bam
And I get a message saying [W::sam_read1] parse error at line 1 [bam_sort_core] truncated file. Aborting.
What's going wrong? Thanks for your help.
It's the bam file that needs to be sorted and indexed, which you can do using samtools. Don't try to sort the gff files or genomes! But I'm not sure if you can do what you want to do in IGV. It is for displaying bam files (made of mapped reads) against a genome, not for comparing genomes or genome annotations to each other. It sounds like what you need to do is to run a multiple sequence alignment on the gene of interest, which you should be able to get from a transcriptome file rather than the whole genome.
I'm getting the genomic data from Phytozome. All the files are .gff3 or .fa, none come as .bam.
I really just need to get the sequence for a certain location on the chromosome from the 3 versions of the genome, and then align them all. I thought IGV would let me get the sequences out of these files... If I can just get the 3 versions of the sequence for this locus, I'll have everything I need. Where should I go from here?
I'll be doing the same thing with the transcriptomic data, but I know there's a flaw in the transcriptomic data for this gene of interest so I want to look at the genomic DNA first. Thanks for your quick response and your help.
IGV is designed for viewing bam files, but you can just use it to look at the gene annotations if you don't have a bam file. Go to file -> load genome from file (NOT "load from file") -> pick the fasta file. Then I think you can drag and drop a gff3 on top of it. Alternately, it looks like you can merge them together into a .genome file with file -> import genome -> select the fasta file, and under optional, select the gff3 file for gene file. Then you should be able to zoom in and scroll around and look at the annotations, even though there is no bam file. I've never done this, though, so let me know if it works.
There is no "load genome from file" on my file menu. I'm running IGV 2.3.78 on a Mac.
edit: Ah, it's in the genome menu. I'll try this out and report back
edit2: Okay, I can load the FASTA but I'm having a hard time loading the .gff3. There is no "import genome" on my file menu and if I try to load the .gff3 from a file, I first get a message saying an index file must be created, then I get a message saying the .gff3 must be sorted.
How do I put the .gff3 and .fa together so that I can look up a certain gene and the flanking sequence? I will do this for 3 different versions of the .gff3 to look at differences between the 3 versions of the genome annotation. Thanks for your help.