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Alternative splicing analysis

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.

rna-seq
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updated by CriticalPeriod • CriticalPeriod • written by a210c452 • a210c452

how about this one: findAS ... not sure how good/feasible/performant/maintained it is though

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written by lieven.sterck lieven.sterck

I was wondering the same, if someone can help ? for some reason, it doesn't work on IGV with my data ...

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written by CriticalPeriod • CriticalPeriod

Please use comment instead of answer, if you are not answering the question. Thanks.

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written by Benn Benn

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-map as 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

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written by michael.ante michael.ante

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?

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written by Friederike Friederike

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