Question: How to prepare a BED file to make a sashimi plot in IGV?
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gravatar for Joseph Hughes
3.2 years ago by
Joseph Hughes2.7k
Scotland, UK
Joseph Hughes2.7k wrote:

Using bowtie and a number of scripts, I have determined the position of donor and acceptor sites in a virus genome and the number of reads that span these sites. I have read through the documentation for MISO and how to use it to produce sashimi plots however in my particular case, I do not want to re-process the BAM file, generate a gff file etc... I would like to produce from the data I have on the donor and acceptor sites, the input for IGV that will enable me to draw a sashimi plot. 

I think it is possible to do this using a BED file but I am obviously putting information in the wrong fields as I am not able to get the arcs linking up different sites using the sashimi plot options.

UPDATE: It is not possible to create a sashimi plot from just a bed file. The SAM/BAM file is needed.

 

igv sashimi bed • 1.7k views
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Joseph Hughes2.7k
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