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Old 12-11-2012, 08:49 AM   #1
TabeaK
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Default Annotation viewing in IGV/Tablet - how to create an alias file

Hello everyone!

The problem of the day that has me a little stymied is the following:

I try to visualise a large alignment (bam file) in either IGV or tablet.

I have tried to upload the feature file (GFF3); to help me navigate. No luck.

My suspicion is; that the name of the contigs does not match between genome reference and gff.

My reference genome is a whole genome shotgut assembly consisting of a ton of scaffolds.

These are named as follows (example): gi|123456789|ref|NW_123456789.1|

They are also showing up in my bam file; so all good there!

The gff file, if I interpret it correctly; only uses the NW_123456789.1 part as the reference; which is why I assume tablet and IGV cannot recognize the features.

Now, the solution would be to create an alias file. But, how do I do it? I have 100.000 odd scaffolds; doing it by hand is out of the question...

Last edited by TabeaK; 12-11-2012 at 12:41 PM.
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Old 12-12-2012, 06:54 AM   #2
Jim Robinson
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Hi,

What version of IGV are you using? It should automatically recognize and alias identifiers of that sort.

I'm sure there are more direct ways to do this, but this method works. First cut out the short identifiers like this

cut -f 4 -d '|' inputFile > names.txt

Then paste the file together

paste inputFile names.txt > yourGenome_alias.tab

Jim
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Old 12-12-2012, 08:26 AM   #3
TabeaK
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Ho Jim; thanks for your answer!

I am running version 2.1.28 on MacOSX 7.4.

Working brilliantly (great tool!); apart from viewing annotations.

I'll try your suggestion and report back.
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Old 12-12-2012, 08:41 AM   #4
Jim Robinson
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I'm a bit puzzled because the aliasing should not be necessary in this case. This is done automatically for sequences that start with "gi|". So gi|123456789|ref|NW_123456789.1| should automatically resolve to NW_123456789.1. If you want to send me a short snippet of your fasta file, and some sample of your gff3, I will look into this further. You can send it to igv-team@broadinstitute.org.
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Old 12-12-2012, 09:25 AM   #5
TabeaK
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Thanks for the offer! I'll email you a bit of data from both fasta and gff ASAP.
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