Last updated: 2022-06-13
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Knit directory: rotation2/
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rsync -a hchen131@midway2.rcc.uchicago.edu:/project2/xuanyao/data/Morris_2021 ~/Desktopcd ~/rotation2/
[ ! -d ../Morris_2021/fastqc_results/ ] && mkdir ../Morris_2021/fastqc_results/
fastqc --threads 16 ../Morris_2021/STINGseq_Morris_2021_raw/*.fastq.gz --outdir=../Morris_2021/fastqc_results/Sample SRR14141135:
- SRR14141135_1
- SRR14141135_2
Sample SRR14141136:
- SRR14141136_1
- SRR14141136_2
Sample SRR14141137:
- SRR14141137_1
- SRR14141137_2
Sample SRR14141138:
- SRR14141138_1
- SRR14141138_2
Sample SRR14141139:
- SRR14141139_1
- SRR14141139_2
Sample SRR14141140:
- SRR14141140_1
- SRR14141140_2
Sample SRR14141141:
- SRR14141141_1
- SRR14141141_2
Sample SRR14141142:
- SRR14141142_1
- SRR14141142_2
Sample SRR14141143:
- SRR14141143_1
- SRR14141143_2
Sample SRR14141144:
- SRR14141144_1
- SRR14141144_2
Sample SRR14141145:
- SRR14141145_1
- SRR14141145_2
Sample SRR14141146:
- SRR14141146_1
- SRR14141146_2
1226bp or 57bp
(why?)30-35x~40 bp)sudo apt-get update && sudo apt-get install libgeos-dev -y
sudo -i R
installe.packages("Seurat")
q()f_exp_matrix <- Seurat::ReadMtx(mtx = "../Morris_2021/GSM5225857_cDNA.mtx",
features = "../Morris_2021/GSM5225857_cDNA.features.txt",
cells = "../Morris_2021/GSM5225857_cDNA.barcodes.txt",
cell.column=1,
feature.column=1,
mtx.transpose=T)
f_grna_matrix <- Seurat::ReadMtx(mtx = "../Morris_2021/GSM5225858_GDO.mtx",
features = "../Morris_2021/GSM5225858_GDO.features.txt",
cells = "../Morris_2021/GSM5225858_GDO.barcodes.txt",
cell.column=1,
feature.column=1,
mtx.transpose=T)
sessionInfo()R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] workflowr_1.7.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.8.3 bslib_0.3.1 compiler_4.2.0 pillar_1.7.0
[5] later_1.3.0 git2r_0.30.1 jquerylib_0.1.4 tools_4.2.0
[9] getPass_0.2-2 digest_0.6.29 jsonlite_1.8.0 evaluate_0.15
[13] tibble_3.1.7 lifecycle_1.0.1 pkgconfig_2.0.3 rlang_1.0.2
[17] cli_3.3.0 rstudioapi_0.13 yaml_2.3.5 xfun_0.31
[21] fastmap_1.1.0 httr_1.4.3 stringr_1.4.0 knitr_1.39
[25] sass_0.4.1 fs_1.5.2 vctrs_0.4.1 rprojroot_2.0.3
[29] glue_1.6.2 R6_2.5.1 processx_3.6.0 fansi_1.0.3
[33] rmarkdown_2.14 callr_3.7.0 magrittr_2.0.3 whisker_0.4
[37] ps_1.7.0 promises_1.2.0.1 htmltools_0.5.2 ellipsis_0.3.2
[41] httpuv_1.6.5 utf8_1.2.2 stringi_1.7.6 crayon_1.5.1