ShouWenWang
commented
3 weeks ago The snakemake_DARLIN has two ways to analyze the CARLIN data. 1, the matlab way. It relies on the matlaib CARLIN pipeline. To modify the reference sequence, you need to change it here: https://github.com/ShouWenWang-Lab/Custom_CARLIN/tree/main/%40CARLIN_def https://github.com/ShouWenWang-Lab/Custom_CARLIN/tree/main/cfg This change is big and challenging.
2, there is also a python based method. This method, however, does not call mutations in the sequence like the matlab way. It only identifies the DARLIN sequence, and use difference sequences to call different clones. We implemented a single-cell version. But changing it to bulk should be also easy. https://github.com/ShouWenWang-Lab/snakemake_DARLIN/blob/master/QC/single_cell_DARLIN-10x.ipynb
-- Shou-Wen Wang, Ph.D. Principal Investigator School of Life Sciences | School of Science Westlake University Shilongshan ST #18, Xihu, Hangzhou, Zhejiang https://www.shouwenwang-lab.com/
From: Jiazheng Pei @.> Date: Friday, June 14, 2024 at 10:45 AM To: ShouWenWang-Lab/snakemake_DARLIN @.> Cc: Subscribed @.***> Subject: [ShouWenWang-Lab/snakemake_DARLIN] Does the python pipeline include sequence alignment and allele calling functions? (Issue #8)
Hi! Thanks for providing a python-based version of CARLIN pipeline. We want to modify the arguments to run on our own sequencing data and reference from a different experiment protocol. However, I can't locate where the function for sequence alignment is. It seems that the MosaicLineage directly inputs the matlab object from the original CARLIN pipeline? Thanks!
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peipp410
jzussman
Hi! Thanks for providing a python-based version of CARLIN pipeline. We want to modify the arguments to run on our own sequencing data and reference from a different experiment protocol. However, I can't locate where the function for sequence alignment is. It seems that the MosaicLineage directly inputs the matlab object from the original CARLIN pipeline? Thanks!