I've been browsing different papers and publications and trying to figure out what's the best way to analyze data with UMIs.
So far I have used GATK to do some analysis couple of times, but other than that I was mostly playing with alternative splicing analysis so I'm rather new to this CNV calling with UMIs topic and area of research.
What I would like to do is have the following design.
adaptor-UMI-DNAlibraryINSERT-UMI-adaptor
The UMIs will be 5 random bases on each side.
I get the whole UMI thinking and analysis but what I haven't found yet is the software to do such analysis. I've seen few tools to mark/find UMIs and put them on the header of the fastq sequence but then what? How do you bin and get rid of the true PCR duplicates? Does Picard have a function for it? If I have to write my own code then I'm out of luck lol.
I know Agilent supports UMIs with their Haloplex HS kits and their Surecall software that is mostly (from what I've heard) a nice GATK GUI.
Any help and guidance would be much appreciated. Newbies have the right to learn too, right?
Thank you in advance
So far I have used GATK to do some analysis couple of times, but other than that I was mostly playing with alternative splicing analysis so I'm rather new to this CNV calling with UMIs topic and area of research.
What I would like to do is have the following design.
adaptor-UMI-DNAlibraryINSERT-UMI-adaptor
The UMIs will be 5 random bases on each side.
I get the whole UMI thinking and analysis but what I haven't found yet is the software to do such analysis. I've seen few tools to mark/find UMIs and put them on the header of the fastq sequence but then what? How do you bin and get rid of the true PCR duplicates? Does Picard have a function for it? If I have to write my own code then I'm out of luck lol.
I know Agilent supports UMIs with their Haloplex HS kits and their Surecall software that is mostly (from what I've heard) a nice GATK GUI.
Any help and guidance would be much appreciated. Newbies have the right to learn too, right?
Thank you in advance
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