Hi, everyone,
I have the bed file in such kind of format:
ENSMUSG00000025925 15805904 15805932 cds
ENSMUSG00000045216 36106069 36106094 utr3
ENSMUSG00000001138 36513045 36513067 cds
ENSMUSG00000065629 39519551 39519648 cds
ENSMUSG00000026074 39997066 39997110 cds
ENSMUSG00000073676 55091153 55091195 utr3
ENSMUSG00000026020 59691944 59692011 intron
ENSMUSG00000077345 59691944 59692011 cds
ENSMUSG00000026020 59692554 59692579 intron
Does there have easily way to graw the region in each gene, like:
it's not the real gene structure, but the distribution of the peaks above each gene. THX
1 answer
You should be able to convert the BED file to a genbank and then run it through any number of browsing/plotting tools is one option.
Edit:
I thought this would be simple but I misread the title of the link I originally posted as Genomax pointed out, so you might have to code up something yourself (unless you/someone finds one!)
Here's a naive and high-level approach that might work:
Using (Bio)Python's index slicing notation you'll be able to pass your bed file coordinates to pull out the relevant sections from the original sequence to which they pertain.
You'll probably need the full sequence to insert in to the genbank (or at least the maximal extents of your features).
You can then build up a custom SeqRecord, adding your pairs of BED coordinates as new features, with the corresponding feature info from your right hand column.
Once that's all done, you can use SeqIO to write out your custom SeqRecord as a Genbank, and then use something like SnapGene/Artemis/JBrowse... or whatever your preferred sequence browsing/visualisation tool is.
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