Question: Alternative splicing analysis
0
gravatar for a210c452
10 months ago by
a210c4520
a210c4520 wrote:

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 • 549 views
ADD COMMENTlink modified 5 months ago by CriticalPeriod0 • written 10 months ago by a210c4520
1

Some options to consider while you wait for an answer: alternative splicing analysis There is also cufflinks (http://cole-trapnell-lab.github.io/cufflinks/ )

ADD REPLYlink modified 10 months ago • written 10 months ago by genomax69k

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

ADD REPLYlink written 10 months ago by lieven.sterck5.5k

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

ADD REPLYlink written 5 months ago by CriticalPeriod0

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

ADD REPLYlink modified 5 months ago • written 5 months ago by Benn7.1k

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

ADD REPLYlink modified 4 months ago • written 5 months ago by michael.ante3.3k

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?

ADD REPLYlink written 5 months ago by Friederike4.5k
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