Hg19 LncRNA

[Jennifer Di Tommaso]

Hi all,

I am sorry if maybe I am not the first one with this question.

I would like to see some alignment files using IGV, but I am mainly interested in non-coding RNA (such as lncRNA or miRNA). 

Is there a way to increase the number of transcripts showed in the feature track, including all the transcripts now annotated?

In other words, I expect to see lncRNA in some regions, I have the aligned reads there and I know that there is the lncRNA X in that position, but loading hg19 I can not see the exon/intron representation in the genome, in the lower track, is there a way to add these kind of information?

Thank you in advance for your reply and please let me know if my question is not clear, I will try to explain in a better way.

Kind regards,

Jennifer

[Jim Robinson]

You can load your own annotation files in  bed, gff, or gtf formats.   Can you give me a specific locus that is missing a lncRNA?  

Jim

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[Jennifer Di Tommaso]

Dear Jim,

some examples are:

AC104820.2

IL21-AS1

AC007278.3

RP3-395M20.8

These are examples that are probably only present in the V19 Gencode annotation, not the well-defined Refseq one. The UCSC browser does recognise them as part of the Basic Gene Annotation Set from GENCODE Version 19.

So, when I load the Hg19 I can clearly see them in my alignments but not in the annotation track and I am not sure about which file I should load to correctly see those lncRNA and the genes.

Thank you!

Jennifer

[Jim Robinson]

OK,  I'll look into this when I return next week, traveling now.  You can  get the gencode annotations as "gff" files but they are huge,  the steps would be to (1) download the gff file,  (2) sort the file with igvtools,  (3) index the file, then load it.   You can run igvtools from the "Tools" menu.   Alternatively you could use "tabix" to index the file.

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