https://github.com/likelet/script_for_ld_crispr
a set of script for processing a cripr result from LD library
https://github.com/likelet/script_for_ld_crispr
Last synced: 14 days ago
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a set of script for processing a cripr result from LD library
- Host: GitHub
- URL: https://github.com/likelet/script_for_ld_crispr
- Owner: likelet
- Created: 2021-09-19T08:00:23.000Z (almost 5 years ago)
- Default Branch: main
- Last Pushed: 2021-12-27T15:15:32.000Z (over 4 years ago)
- Last Synced: 2025-11-19T10:22:26.860Z (8 months ago)
- Language: R
- Size: 4.88 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# script_for_LD_Crispr
This repo presents the scripts used for processing a sequencing reads from crispr screen assay.
the script consists of tree steps including
- 1 grep index of samples with the mixed library
- 2 obtain the sgRNA sequences based on INDEX+PRIMER sequences grep result .
- 3 count the sgRNA frequnces and annotate the result with known librarys
to note, as the raw count could not be directly compared, we then normalized the reads with total library and time a 10^6 allowing directly comparison among samples.
The main process steps were processed with `SeqKit` tool and `csvtk` which developed by Wei Shen
# authors
Qi ZHao