What packages/tools are available to use SJ.out.tab file obtained from STAR

Question

[rohitsatyam102]

Hi everyone.

I have these Sj.out.tab files obtained from STAR and am aware that these files contain high confidence collapsed splice junctions. However, I failed to find tools/R packages that take these files as input and help you do some meaningful analysis like differential splicing. Can you point me to some papers that have used these files for similar kind of analysis or can suggest packages that use these files?

Answer 1

[brown.annaleigh]

Hi there,

You can check this out. https://github.com/dzhang32/dasper/

But most tools I believe are developed to work with the aligned data, the BAM files that STAR produced, and then you can hunt through the splice junctions afterwards when you know more what you're looking for.