GFF/GTF tracks

[Laura Vengadabady]

Hi,

I am trying to load a gtf file that I made. Everything loads perfectly
except for two things:

1) IGV produces its own gene ids (e.g.: igv_ad47eb4a-
eb69-4c95-9254-89891e42f18a)
and that is what appears on the track. It is only when I click on the
gene that I am able to view the ID that I have set. How can I change
the igv ids for my own?

2) One of the attributes values in the attribute field (last columns
of .gtf file) contains a space and is truncated straight after. Is
there a way to avoid this?

Many thanks,

Laura

[Jacob Silterra]

Hello Laura,

1) What is the tag you are using to specify the id? If IGV does not find an ID it generates a random one. The recognized ID fields are those used for GFF2, if you can use the key "ID" which works for both GFF2 and GFF3.

2) If the attributes field contains spaces it must be surrounded by quotes. Personally I would recommend against using spaces, replacing with an underscore might be better, but surrounding the attribute field with quotes should work.

-Jacob

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Jacob Silterra
Software Engineer
Broad Institute