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fanglab / SMRTER

Single Molecule Real Time sequencing Epigenetic Refinement
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in-silico control #3

Open cascoamarillo opened 5 years ago

cascoamarillo commented 5 years ago

Dear developers, Thank you for these PacBio-universe tools. I have one question, but it is not a code issue: in this SMRTER tool it's mentioned the option of using an in-silico control. Since I don't have a natural/traditional (wga) control for my data; how can it be generated? I have just looking around (SMRT analysis software) but couldn't find it.

One more thing, in the paper Beaulaurier et al. 2015 when looking at scores it is mentioned the creation of a negative control, instead of a wga, by randomly shuffling IPD values among molecules. Are we taking about the same type of control (in-silico=shuffling IPD)? Thank you for your time. Best

fanggang commented 5 years ago

Thank you for your interest. The in silico option is what we do plan to enable and it will hopefully be available in 2019. In silico model is based on predicted IPDs for genome sequences (different from shuffled IPDs).

On Dec 19, 2018, at 11:15 AM, cascoamarillo notifications@github.com wrote:

Dear developers, Thank you for these PacBio-universe tools. I have one question, but it is not an code issue: in this SMRTER tool it's mentioned the option of using an in-silico control. Since I don't have a natural/traditional (wga) control for my data; how can it be generated? I have just looking around (SMRT analysis software) but couldn't find it.

One more thing, in the paper Beaulaurier et al. 2015 when looking at scores it is mentioned the creation of a negative control, instead of a wga, by randomly shuffling IPD values among molecules. Are we taking about the same type of control (in-silico=shuffling IPD)? Thank you for your time. Best

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cascoamarillo commented 5 years ago

Thank you so much for the quick reply! Please, let me ask one more thing. Maybe, this would be more related with your other distribution, SMALR. Following then shuffling IPD values randomly; is it done on the alignment file .cmp.h5? Any tips on this would be appreciated. Thanks.

fanggang commented 5 years ago

Oops. Apologies. My last reply was actually meant for SMALR, for which we got multiple requests for in silico. To clarify, for SMRTER, an WGA control is highly recommended.

On Dec 19, 2018, at 4:33 PM, cascoamarillo notifications@github.com wrote:

Thank you so much for the quick reply! Please, let me ask one more thing. Maybe, this would be more related with your other distribution, SMALR. Following then shuffling IPD values randomly; is it done on the alignment file .cmp.h5? Any tips on this would be appreciated. Thanks.

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