Last updated: 2021-02-15
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Knit directory: Mouse_AAV_PGR_RNAseq_bulk/
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Nuclei RNA-seq generates sequencing reads that map across a whole gene (intron and exon) and therefore a nuclei-specific reference genome is generated for sequencing read counting.
#!/bin/bash
grep -w gene Mus_musculus.GRCm38.96.gtf | cut -f1,4,5,7,9| cut -d '"' -f-2,6 \
| sed 's/gene_id "//' | tr '"' '_'\
| awk '{OFS="\t"} {print $5,$1,$2,$3,$4}' > Mus_musculus.GRCm38.96.fulllength.saf
grep: Mus_musculus.GRCm38.96.gtf: No such file or directory
sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /hpc/software/installed/R/3.6.1/lib64/R/lib/libRblas.so
LAPACK: /hpc/software/installed/R/3.6.1/lib64/R/lib/libRlapack.so
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_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 rstudioapi_0.11 whisker_0.4 knitr_1.30
[5] magrittr_1.5 R6_2.5.0 rlang_0.4.7 stringr_1.4.0
[9] tools_3.6.1 xfun_0.18 git2r_0.27.1 htmltools_0.5.0
[13] ellipsis_0.3.1 rprojroot_1.3-2 yaml_2.2.1 digest_0.6.27
[17] tibble_3.0.3 lifecycle_0.2.0 crayon_1.3.4 later_1.1.0.1
[21] vctrs_0.3.2 promises_1.1.1 fs_1.5.0 glue_1.4.2
[25] evaluate_0.14 rmarkdown_2.5 stringi_1.5.3 compiler_3.6.1
[29] pillar_1.4.6 backports_1.1.10 httpuv_1.5.4 pkgconfig_2.0.3