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pachterlab / kma

Keep Me Around: Intron Retention Detection
GNU General Public License v2.0
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HISAT2 - cufflinks #3

Open vmanders opened 8 years ago

vmanders commented 8 years ago

I would like to use KMA, but I use HISAT2 and cufflinks for the alignment and quantification. How can I implement KMA in this pipeline for intron retention detection?

Thanks in advance!

pimentel commented 8 years ago

Due to the way that cufflinks works (at the genome level rather than the transcript level), it is possible to include into kma. Quantification tools such as kallisto and RSEM are compatible , but haven't been integrated yet. They will be in the (distant) future

federicomarini commented 8 years ago

Hey Harold, I just wanted to follow up on this topic. Is there any news on having kallistofor the initial quantification to plug into kma? I would really like to do it - maybe it is more straightforward than what I can expect and try to write my own methods for it?

pimentel commented 8 years ago

@federicomarini integrating into the existing kma actually should be fairly easy to. I've been pretty busy as I am trying to wrap up sleuth and also graduate, so this has been fairly low priority for me.

Perhaps the biggest issue with the existing kma is that it hasn't really been tested in a number of different conditions, so as people have been experiencing, it will likely fail with different types of transcriptomes when trying to pull out the relevant intronic regions. This should be reengineered to make a robust production version (this is in my queue for late Summer). If you are interested in helping, perhaps you can speed up the process. Mind sending me an email if you are interested? Perhaps we could setup a skype call.

haroldpimentel@gmail.com

federicomarini commented 8 years ago

@pimentel You'll soon have an email. Thanks for the positive reply!