03/26/2021:

```
# Filter out raw data that do not contain linker sequence
# edit 00_1.qc_raw_data_L1.sh & 00_2.qc_raw_data_L2.sh for each sample
sbatch 00_1.qc_raw_data_L1.sh
sbatch 00_2.qc_raw_data_L2.sh
```

```
# Rearrange UMI/barcode compatible for st-pipeline
# edit 1-effective.sh
dSQ --job-file 1-effective.sh --mail-type=ALL --partition=scavenge --cpus-per-task=16 --mem-per-cpu=4g --submit
```

```
# Alignment
# for 2-align-step1.pl
wget https://cpan.metacpan.org/authors/id/M/MA/MANWAR/SVG-2.85.tar.gz
tar -zxvf SVG-2.85.tar.gz
module load Perl/5.28.0-GCCcore-7.3.0 #have to run this for all related to perl
perl Makefile.PL INSTALL_BASE=/gpfs/ysm/project/fan/gs592/Database/PerlScripts/perl_install/SVG-2.85/mybuild
make
make install
export PERL5LIB=/gpfs/ysm/project/fan/gs592/Database/PerlScripts/perl_install/SVG-2.85/mybuild/lib/perl5:$PERL5LIB
```

```
# st-pipeline
# edit 2-st-pipeline.sh & stp.sh
srun --pty -p interactive -c 8 --mem=64g bash
module load miniconda
conda activate st-pipeline
dSQ --job-file stp.sh --mail-type=ALL --partition=scavenge --cpus-per-task=16 --mem-per-cpu=4g --submit
# edit converttonames.sh
sh converttonames.sh
```

# 07/08/2021
# Updating Seurat package removed my.background argument in SpatialPlots
# To fix:
# run 
# install.packages("/gpfs/ysm/project/fan/gs592/RStudioScripts/seuratpkg-cust/seurat.tar.gz",repos=NULL, type = "source")

# 12/16/2021
# Install clusterProfiler package
# run below
packageurl <- "https://cran.r-project.org/src/contrib/Archive/rvcheck/rvcheck_0.1.8.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
remove.packages("clusterProfiler")
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("clusterProfiler")


# 09/14/2022
# creating new conda environment for RStudio on Yale HPC
srun --pty -p interactive bash
module load miniconda
mamba create -n ~env-name~ r-base=4.0 r-essentials r-raster r-rgdal python
conda activate ~env-name~
pip install magic-impute
mamba install cmake
mamba install r-devtools
# in R
R
install.packages("pacman")
install.packages("BiocManager")
install.packages("Rmagic")
devtools::install_github("gadenbuie/rsthemes")
#devtools::install_github("aertslab/cisTopic")
library(rsthemes)
rsthemes::install_rsthemes()
pacman::p_load(~your_packages~)
~~request 4 CPUs 16GB each~~ rstudio 1.417