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IGV likes its reference genome files in GFF (Gene Feature Format). Unfortunately, our old friend bp_seqconvert.pl doesn't do GFF. Fortunately, it's cousin bp_genbank2gff3.pl does with So, we're going to show you another tool for sequence format conversion called Readseq.

Readseq is written in java. To use it you need to first [download the file readseq.jar linked from here|Readseq.

To get this onto TACC easily, use:

Code Block

wget http://iubio.bio.indiana.edu/soft/molbio/readseq/java/readseq.jar

The general command to run the software is:

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module load java
java -jar readseq.jar
java -cp readseq.jar run

(Why the module load and funny invocation? You are actually using the command java and telling it where to find a "jar" file of java code to run. The -jar and -cp options run it in different ways. It's pretty confusing.)

To do the conversion that we want, use this command:

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bp_genbank2gff3.pl
java -cp readseq.jar run NC_012967.1.gbk -f GFF -o test.gff

java -cp readseq.jar run NC_012967.1.gbk
Expand
Where's the output?Where's the output?
-f GFF -o NC_012967.1.gbk.gff

It's a bit hard to figure out because it takes the unnamed arguments before the optional flag arguments and there is no example command and you have to switch -jar to -cp. Search online for usage examples when you can't figure something out from the help.

Take a look at the contents of the original Genbank file and the new GFF3 GFF file and try to get a handle on what is going on in this conversion.(NB: I had to "fix" bp_genbank2gff3.pl to work on our GenBank file, by removing a line in the Perl script that caused an error. If someone knows of an easier way to get a GFF file from a file downloaded from Genbank, please share!)

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Side-note on displaying BLAST results as GFF files in IGV or other browsers
Side-note on displaying BLAST results as GFF files in IGV or other browsers

Another useful trick with either IGV or UCSC: displaying your own BLAST results: BioPerl allows for super-easy conversion from blast output to a gff file; IGV and the UCSC browser both understand GFF files. The short script bl2gff.pl does the conversion.

Let's use the blast result we had from the earlier test for the JAG1 gene to show you how. You'll need to provide the input file - it's the ".oNNNNNN" output file from your blast job.

Code Block
titleDisplaying BLAST results in IGV or UCSC
grep '^gi' blast_jag1.o586038 > jag1_blast.out
module load perl
module load bioperl
bl2gff.pl jag1_blast.out > jag1_blast.out.gff

The resulting jag1_blast.out.gff can be moved to your local machine and opened in IGV. Load the human reference first though!

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