User: jhanks1981

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jhanks19810
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Posts by jhanks1981

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Comment: C: Why can't I use a GRanges txDb with clusterMap function? (as input or output)
... Apologies if this is a naive question, but is that something I can do something about? ...
written 4 months ago by jhanks19810
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Why can't I use a GRanges txDb with clusterMap function? (as input or output)
... I need to create several transcript database objects from different GTF files, so I would like to save time by running each txdb creation in parallel. However, the txdb that is generated when I have run it in parallel (although it completes without errors) doesn't behave like the one generated by ...
R parallel genomicfeatures clustermap written 4 months ago by jhanks19810
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Comment: C: Custom features in IGV
... Interesting. I am on version 2.3.97 for Linux. Is there a better/more consistent viewer than IGV? ...
written 8 months ago by jhanks19810
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Comment: C: Custom features in IGV
... 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! ...
written 8 months ago by jhanks19810
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Comment: C: Custom features in IGV
... Sorry, the link was in the raw post, but for some reason it didn't show. The "Custo," was supposed to be "Custom". ...
written 8 months ago by jhanks19810
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Custom features in IGV
... 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 an ...
gtf features igv written 8 months ago by jhanks19810 • updated 8 months ago by Dan D6.4k

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