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docs/content/Notes/Tsai.rst

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+Tsai Lab Bioinformatics
+=======================
+
+Protein mutagenesis
+^^^^^^^^^^^
+
+Code: https://github.com/tsailabSJ/Cas9Variants/tree/master/Mammalian_system
+
+1. Dictionary generation
+---------------------
+
+See ``PacBio_amplicon_sequencing`` folder. The code was originally written for Cas9 (Kasey), recently adapted to PE/RT (Kiera).
+
+
+Kiera's data is large, I have to split the reads and run the pipeline individually. use ``split.sh`` to split the reads.
+
+Kasey dict: /research_jude/rgs01_jude/groups/tsaigrp/projects/Genomics/common/projects/Cas9mutagenesis/pacbio_230301_293246_tsaigrp_Amplicon/pacbio_cas9mut_amp_yli11_2023-07-13
+
+KJ001.read_stat.csv.all_dictionary.tsv
+
+KJ002.read_stat.csv.all_dictionary.tsv
+
+Kiera dict: /research_jude/rgs01_jude/groups/tsaigrp/projects/Genomics/common/projects/pacbio/825386_tsaigrp_Amplicon_Kiera/create_barcode_yli11_2024-05-22
+
+2. Compare enrichment of mutagenesis assay
+----------------------
+
+See ``main_v2.lsf`` pipeline description. Code is generic to Cas9 or PE/RT.
+
+Usually Kesey run this pipeline herself. Sometimes error happens when the input format is wrong, e.g., upper-case lower-case, tab/space, name not match in ``fastq.tsv`` and ``design_matrix``. 
+
+Interactive heatmap is generated by the pipeline. This is how to run it manually.
+
+::
+
+	src=/home/yli11/Tools/Cas9Variants/Mammalian_system
+
+	module load conda3/202011
+
+	source activate /home/yli11/.conda/envs/captureC
+
+	cd {{jid}}
+
+	comparison=${COL1}_vs_${COL2}
+
+	interactive_heatmap.py -f $comparison.AA_compare.csv --reformat_config liyc --header -o $comparison.AA_compare.interactive.html
+
+
+PAM specificity assay
+^^^^^^^^^^^^
+
+code: https://github.com/tsailabSJ/LentiviralPAMspecificity
+
+1. Dictionary generation
+---------------------
+
+
+
+2. Calculate enrichment
+----------------------
+
+
+
+
+Pooled-GUIDE-seq
+^^^^^^^^^^^^
+
+pooled gRNA design: /research_jude/rgs01_jude/groups/tsaigrp/projects/Genomics/common/projects/Azusa_pooled_GUIDE
+
+code: ``guideseq_pool_gRNA_design_given_genes.py``  ``guideseq_pool_gRNA_design.py``
+
+``guideseq_pool_gRNA_design_given_genes.py`` is unfinished I think.
+
+This is how I used to generate the library:
+
+::
+
+	module load conda3/202011
+
+	source activate /home/yli11/.conda/envs/captureC
+
+	guideseq_pool_gRNA_design.py -h
+
+	guideseq_pool_gRNA_design.py -i tcell_exon.bed --sample 21083 -o guideseq_pool_run1.csv
+
+
+GUIDE-seq, CHANGE-seq, CHANGE-seq BE
+^^^^^^^^^^^^
+
+They all know how to run them.
+
+CHANGE-seq-BE:/research_jude/rgs01_jude/groups/tsaigrp/projects/Genomics/common/src/changeseq_py3
+
+GUIDE-seq:/research_jude/rgs01_jude/groups/tsaigrp/projects/Genomics/common/src/changeseq_py3
+
+
+CHANGE-seq:/research_jude/rgs01_jude/groups/tsaigrp/projects/Genomics/common/src/changeseq
+
+
+
+PARADIGM
+^^^^^^
+
+variant design code: /research_jude/rgs01_jude/groups/tsaigrp/projects/Genomics/common/projects/Paradigm/Yichao_code
+
+pipeline code: https://github.com/tsailabSJ/PARADIGM_code
+
+R code to calculate different crisprscores
+
+cutadapt used to extract variable sequence given two flanking sequences
+
+Genetic variation
+^^^^^^^^^^
+
+
+data and code: /research_jude/rgs01_jude/groups/tsaigrp/projects/Genomics/common/projects/GUIDEseq/02172023_GUIDEseq2_GV_Novaseq
+
+
+
+randomized CHANGE-seq
+^^^^^^^^^^
+
+code: https://github.com/tsailabSJ/changeseq_randomized
+
+/research_jude/rgs01_jude/groups/tsaigrp/projects/Genomics/common/projects/CHANGE_seq/liyc_Mixed_Base_analysis
+
+Usually Ashely run this pipeline herself.
+
+
+