Show genome coverage in IGV-browser
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12 weeks ago

Hi everyone! I have a genome .fa file and a .bed file showing repetitive elements in this genome. I want to visualize these files in IGV to see how genome is covered by repetitive DNA. If I do it in scale of all genome ( picture 1) it works, but if I zoom in the chromosome it does not work (picture 2). Does anyone know how to add a track, or may be do something else to display the coverage/density plot?

Picture1:

Picture2:

assembly annotation igv • 497 views
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Can you show a snippet of your BED data? What columns do you have in the file?

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Of course:

X   0   49  Unknown
X   18  110 Unknown
X   2711    2879    DNA/DTC
X   2730    3146    DNA/Helitron

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Looks like you only have intervals in your file so where is the "coverage" part going to come from? In Pic 1 when you are fully zoomed out it the "coverage plot" is a visual illusion even though the actual records are just intervals when you zoom in sufficiently i.e. they are just one tick in that track in Pic2.

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But I thought IGV calculates something like coverage for each segment. May be something like coverage (%) per 100 kb.

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Now I added a column and it looks like:

X   0   49  Unknown    0.15692
X   18  110 Unknown   0.15692
X   2711    2879    DNA/DTC   0.15692
X   2730    3146    DNA/Helitron   0.15692


the fifth column is a coverage per bin (100kb window size). Do you know how can I visualize it via IGV?