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Background

We want to be able to load (or request) data for a genome including the sequence and gene annotation (bacteria). Then, we want to load our own annotation which should be displayed as a line plot:

position score
1        5
2        6
etc.

Where each position corresponds to the position in the genome (i.e. FASTA). Something like this:

enter image description here

Question

Is there a tool that can load a genome sequence, gene annotation, and a position ~ score file, which can be displayed as a line plot?

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  • $\begingroup$ Welcome to the site. In order to suggest a good alternative could you comment what do you need this tool for? Why do you need to display the gene annotation? What is the problem with IGV ? (I found the sentence a bit confusing, perhaps if you rephrase it I'll understand it) $\endgroup$
    – llrs
    Commented Oct 11, 2018 at 13:09
  • $\begingroup$ I thought I was clear regarding what I need it for: uploading genome + annotation + own data (position + score). Why gene annotation? Because we want to look whether the the line plot we upload differs between genes and intergenic regions. Just similar as a GC plot beneath the genes and intergenic regions but then with own supplied scores per position. Indeed, I forgot a word in my sentence about IGV @Llopis $\endgroup$
    – KingBoomie
    Commented Oct 11, 2018 at 13:32
  • $\begingroup$ I don't find this question useful. It only helps people who find IGV ugly. Also you don't seem to have researched for other options like IGB. Have a nice day! $\endgroup$
    – llrs
    Commented Oct 11, 2018 at 14:16
  • $\begingroup$ A local tool is fine, with upload I meant uploading it to a tool (perhaps not the best word choice). The screenshot is from a tool which only visualizes a Listeria genome (no other bacteria), but I liked the interface. Currently I'm trying to use IGB @terdon $\endgroup$
    – KingBoomie
    Commented Oct 11, 2018 at 15:07

1 Answer 1

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You can use UCSC genome browser, which supports custom genome sequence and annotation. Specifically, one needs to create a Track Hub to hold genomes and annotations.

Here is an example:

http://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=http://zlab-trackhub.umassmed.edu/yfu/insects/hub.txt&db=hub_129615_cl_v0.8.2

And here is the corresponding hub.txt file holding the metadata, and URLs to actual fasta, bigWig and bigBed files.

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