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SCENIC.Tcell.r
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SCENIC.Tcell.r
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#!/usr/bin/Rscript
# 2021-2-19
# TFs analysis in T cells
#==================================================================================================
# first you have to generate a csv file
# run in R
library(Seurat)
dat <- readRDS("/public/workspace/lily/CTN/version_3_20/data/Tcell.RDS")
# sub.data=subset(dat,cells=which(dat$refine.group.new%in%c("CT.SC.dominant","CTN.dominant","NC.dominant")))
# if the result is all cells with TFs ,so do not subset cells
write.csv(t(as.matrix(dat[['RNA']]@data)),file="/public/workspace/lily/CTN/version_3_20/trajectory/Tcell/all_Tcell.csv")
#===============================================================================================
# run in shell use pyscenic
#===============================================================================================
#!/bin/sh
bytlib load python-3.6.6
/public/workspace/lily/Lung2Brain/inte7/Pyscenic/Scenic/arboreto_with_multiprocessing.py \
-o /public/workspace/lily/CTN/version_3_20/trajectory/Tcell/all_Tcell.adjacencies.csv \
--method grnboost2 \
--seed 12345 \
--num_workers 5 \
/public/workspace/lily/CTN/version_3_20/trajectory/Tcell/all_Tcell.csv \
/public/workspace/zhumy/ref/SCENIC/hs_hgnc_curated_tfs.txt
echo "step1 done"
sleep 10
pyscenic ctx \
/public/workspace/lily/CTN/version_3_20/trajectory/Tcell/all_Tcell.adjacencies.csv \
/public/workspace/zhumy/ref/SCENIC/hg19-500bp-upstream-7species.mc9nr.feather \
/public/workspace/zhumy/ref/SCENIC/hg19-tss-centered-10kb-7species.mc9nr.feather \
--annotations_fname /public/workspace/lily/Lung2Brain/inte7/Pyscenic/motifs-v9-nr.hgnc-m0.001-o0.0.tbl \
--expression_mtx_fname /public/workspace/lily/CTN/version_3_20/trajectory/Tcell/all_Tcell.csv \
--output /public/workspace/lily/CTN/version_3_20/trajectory/Tcell/all_Tcell_regulons.tsv \
--num_workers 6 \
--mode "custom_multiprocessing"
#=====================================================================================================
echo "step2 done"
sleep 10
pyscenic aucell \
/public/workspace/lily/CTN/version_3_20/trajectory/Tcell/all_Tcell.csv /public/workspace/lily/CTN/version_3_20/trajectory/Tcell/all_Tcell_regulons.tsv \
--output /public/workspace/lily/CTN/version_3_20/trajectory/Tcell/all_Tcell_auc_mtx.tsv \
--num_workers 5 --seed 12345
# pyscenic aucell \
# $expression_mtx_fname $ctx_output \
# --output $aucell_output \
# --num_workers 5 --seed 12345