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6.2 years ago
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Is there an alternative splicing tool that will take in my bam alignment and produce alternative splicing sites? I have alignment files that were produced using rsem and would like to use the alignments for down the road analysis, instead of replicating this effort.
Some options to consider while you wait for an answer: alternative splicing analysis There is also
cufflinks(http://cole-trapnell-lab.github.io/cufflinks/ )how about this one: findAS ... not sure how good/feasible/performant/maintained it is though
I was wondering the same, if someone can help ? for some reason, it doesn't work on IGV with my data ...
Please use
commentinstead ofanswer, if you are not answering the question. Thanks.If you are using rsem, by default you'll be aligning against the transcritome. IGV uses per default a genome reference.
You can use rsem's function
transcript-to-gene-mapas described here. The resulting alignments should be interpreted by IGV.I don't know if it fits your requirements, but have a look at DexSeq.
[Edit:] Missing word
It'd be easier to point to concrete solutions if we knew what exactly the question is that you'd like to address with "alternative splice sites". To begin with, I'm confused about the term -- I know splice sites and I know alternative splicing, which described the phenomenon when two mRNA molecules transcribed from the same gene locus are spliced differently, e.g. by including different exons. What exactly do you mean with alternative splice sites?