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amirmohan / SPROUT

SPROUT is a machine learning tool to predict the DNA repair outcome in CRISPR experiments.
Apache License 2.0
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Can SPROUT output the indel position on the target sequence? #1

Open PEHGP opened 3 years ago

PEHGP commented 3 years ago

dear sir,

Can SPROUT output the insertion/deletion position on the target sequence? Just like FORECasT and inDelphi.

best likuan

amirmohan commented 3 years ago

hi likuan, no the current software outputs the summary statistics of the indels. best, amirali

PEHGP commented 3 years ago

Hi amirali, Thanks for replying. We're very happy to read the SPROUT paper recently, which is also the only model based on testing on primary cells. We really appreciate your state-of-art study for this is a hugh step for applications in real therapeutic scenarios. We're currently investigating gRNA cleavage outcome on postmitotic cells and try to use the non-random editing outcomes to restore frameshift mutations in some non-dividing system. Thus it is important for us to know the detailed editing outcome of selected gRNAs for it define the results of reading-frame correction and will affect the protein sequences after correction. Some pilot study that we had done showed that there are some differences in editing between traditional cell line and postmitotic cell. And the prediction results from inDelphi and FORCasT are more like that from cell line. We believe SPROUT will be more suitable at prediction editing of postmitotic cells for the data trained it is coming from primary T cells. This is the reason we ask whether SPROUT can output the detailed editing product information. Or do you have any suggestions related to this? PS: have you ever compare the outcomes of your large-scale experimental data with the normal cell line, are there any difference? Looking forward to you replying. best, liulian