Question: Custom features in IGV
0
gravatar for jhanks1981
2.3 years ago by
jhanks198110
jhanks198110 wrote:

I am making gtfs file with custom feature types, and I want to inspect them in IGV viewer. However, I cannot view the features if they have a non-standard attribute type (INTRON). However, if I replace the string "INTRON" with "exon", the file displays as expected. Is IGV viewer unable to display anything with a non-standard attribute name, of is there something I am missing? Here are the first two files that demonstrate the issue:

    $ head -5 22_exons.gtf
    chr22   my_calculation  exon    16062326        16062801        .       +       .       gene_id "ENSG00000233866.1"; transcript_id "ENST00000424770.1"; exon_number 1.5; exon_id "no_value"; ccdsid "no_value"; gene_name "no_value"; gene_status "no_value"; gene_type "no_value"; havana_gene "no_value"; havana_transcript "no_value"; level "no_value"; ont "no_value"; tag "no_value"; transcript_name "no_value"; transcript_status "no_value"; transcript_type "no_value";
    chr22   my_calculation  exon    16100658        16101266        .       -       .       gene_id "ENSG00000223875.1"; transcript_id "ENST00000420638.1"; exon_number 3.5; exon_id "no_value"; ccdsid "no_value"; gene_name "no_value"; gene_status "no_value"; gene_type "no_value"; havana_gene "no_value"; havana_transcript "no_value"; level "no_value"; ont "no_value"; tag "no_value"; transcript_name "no_value"; transcript_status "no_value"; transcript_type "no_value";
    chr22   my_calculation  exon    16101484        16118782        .       -       .       gene_id "ENSG00000223875.1"; transcript_id "ENST00000420638.1"; exon_number 2.5; exon_id "no_value"; ccdsid "no_value"; gene_name "no_value"; gene_status "no_value"; gene_type "no_value"; havana_gene "no_value"; havana_transcript "no_value"; level "no_value"; ont "no_value"; tag "no_value"; transcript_name "no_value"; transcript_status "no_value"; transcript_type "no_value";
    chr22   my_calculation  exon    16118923        16122710        .       -       .       gene_id "ENSG00000223875.1"; transcript_id "ENST00000420638.1"; exon_number 1.5; exon_id "no_value"; ccdsid "no_value"; gene_name "no_value"; gene_status "no_value"; gene_type "no_value"; havana_gene "no_value"; havana_transcript "no_value"; level "no_value"; ont "no_value"; tag "no_value"; transcript_name "no_value"; transcript_status "no_value"; transcript_type "no_value";
    chr22   my_calculation  exon    16123778        16124732        .       -       .       gene_id "ENSG00000223875.1"; transcript_id "ENST00000420638.1"; exon_number 1.5; exon_id "no_value"; ccdsid "no_value"; gene_name "no_value"; gene_status "no_value"; gene_type "no_value"; havana_gene "no_value"; havana_transcript "no_value"; level "no_value"; ont "no_value"; tag "no_value"; transcript_name "no_value"; transcript_status "no_value"; transcript_type "no_value";

And this is the same file, except that "exon" is changed to "INTRON"

$ head -5 22_introns.gtf
chr22   my_calculation  INTRON  16062326        16062801        .       +       .       gene_id "ENSG00000233866.1"; transcript_id "ENST00000424770.1"; exon_number 1.5; exon_id "no_value"; ccdsid "no_value"; gene_name "no_value"; gene_status "no_value"; gene_type "no_value"; havana_gene "no_value"; havana_transcript "no_value"; level "no_value"; ont "no_value"; tag "no_value"; transcript_name "no_value"; transcript_status "no_value"; transcript_type "no_value";
chr22   my_calculation  INTRON  16100658        16101266        .       -       .       gene_id "ENSG00000223875.1"; transcript_id "ENST00000420638.1"; exon_number 3.5; exon_id "no_value"; ccdsid "no_value"; gene_name "no_value"; gene_status "no_value"; gene_type "no_value"; havana_gene "no_value"; havana_transcript "no_value"; level "no_value"; ont "no_value"; tag "no_value"; transcript_name "no_value"; transcript_status "no_value"; transcript_type "no_value";
chr22   my_calculation  INTRON  16101484        16118782        .       -       .       gene_id "ENSG00000223875.1"; transcript_id "ENST00000420638.1"; exon_number 2.5; exon_id "no_value"; ccdsid "no_value"; gene_name "no_value"; gene_status "no_value"; gene_type "no_value"; havana_gene "no_value"; havana_transcript "no_value"; level "no_value"; ont "no_value"; tag "no_value"; transcript_name "no_value"; transcript_status "no_value"; transcript_type "no_value";
chr22   my_calculation  INTRON  16118923        16122710        .       -       .       gene_id "ENSG00000223875.1"; transcript_id "ENST00000420638.1"; exon_number 1.5; exon_id "no_value"; ccdsid "no_value"; gene_name "no_value"; gene_status "no_value"; gene_type "no_value"; havana_gene "no_value"; havana_transcript "no_value"; level "no_value"; ont "no_value"; tag "no_value"; transcript_name "no_value"; transcript_status "no_value"; transcript_type "no_value";
chr22   my_calculation  INTRON  16123778        16124732        .       -       .       gene_id "ENSG00000223875.1"; transcript_id "ENST00000420638.1"; exon_number 1.5; exon_id "no_value"; ccdsid "no_value"; gene_name "no_value"; gene_status "no_value"; gene_type "no_value"; havana_gene "no_value"; havana_transcript "no_value"; level "no_value"; ont "no_value"; tag "no_value"; transcript_name "no_value"; transcript_status "no_value"; transcript_type "no_value";

and here is a picture of what I see in IGV with the two files:

https://ibb.co/bCnmP5

Additional details: I am just adding stuff because the forum apparently did not recognize my post as the English language. There is no more relevant information after this. I am just adding sentences because I read that it can help me get past the spam detector. Please forgive this irrelevant stuff. Wow, what an overly aggressive spam detector. My grammar isn't that terrible, is it?

igv features gtf • 965 views
ADD COMMENTlink modified 2.3 years ago by Dan D7.0k • written 2.3 years ago by jhanks198110

You have not attached a link for the image in your post. Can you post a direct link in the body of the text?

Custo, features in IGV

Is that some random text in the title as well?

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by genomax75k

Sorry, the link was in the raw post, but for some reason it didn't show. The "Custo," was supposed to be "Custom".

ADD REPLYlink written 2.3 years ago by jhanks198110

It is not the grammar just too many other types of words in the data I would guess.

ADD REPLYlink written 2.3 years ago by Istvan Albert ♦♦ 81k

I tried your example since I found that surprising and I often have non-standard feature names. For me it does draw lines even when I have the word INTRON as a type.

enter image description here But IGV can be finicky and there are many undocumented features across versions.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Istvan Albert ♦♦ 81k

Interesting. I am on version 2.3.97 for Linux. Is there a better/more consistent viewer than IGV?

ADD REPLYlink written 2.3 years ago by jhanks198110

I would double check that file - it really does not make sense for IGV to now show a feature based on type alone.

I can reason for drawing some differently (CDS are thicker etc) but I doubt that it would be desirable to hide a valid interval from sight. I suspect file format error. Or host your file somewhere and we can check that ourselves.

ADD REPLYlink written 2.3 years ago by Istvan Albert ♦♦ 81k
2
gravatar for Dan D
2.3 years ago by
Dan D7.0k
Tennessee
Dan D7.0k wrote:

The IGV documentation references the official spec for GTF2. That spec only allows for the following values:

  • CDS
  • start_codon
  • stop_codon
  • exon

Granted, the GTF format is a special-case derivation of GFF so that's why it doesn't allow introns as a feature type. I'd think you would be fine if you made the appropriate adjustments and loaded the file as a GFF. Have you tried that?

ADD COMMENTlink written 2.3 years ago by Dan D7.0k

I will try that. Strange though, I've used GTF files with other feature types ("gene", "transcript") without issue. Also, I was reading about the GTF format from here: http://www.ensembl.org/info/website/upload/gff.html

Edit: Yes, that did the trick. Thanks!

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by jhanks198110
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