Last updated: 2018-05-29
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File | Version | Author | Date | Message |
---|---|---|---|---|
Rmd | d58bc13 | Briana Mittleman | 2018-05-29 | start 200 bp analysis |
I will use this analysis to bin the genome into 200bp windows and look at coverage for the 3’ seq libraries for each of these windows. I will use this data then in the leafcutter pipeline to look at differences between data from the total and nuclear fractions.
I performed a similar analysis for the net-seq data so some of the code will come from that. https://brimittleman.github.io/Net-seq/create_blacklist.html
The binned genome file is called: genome_200_wind_fix2.saf, it is in my genome annotation directory.
#!/bin/bash
#SBATCH --job-name=cov200
#SBATCH --time=8:00:00
#SBATCH --output=cov200.out
#SBATCH --error=cov200.err
#SBATCH --partition=broadwl
#SBATCH --mem=20G
#SBATCH --mail-type=END
module load Anaconda3
source activate three-prime-env
#input is a bed file
sample=$1
describer=$(echo ${sample} | sed -e 's/.*\YL-SP-//' | sed -e "s/-sort.bed$//")
featureCounts -T 5 -a /project2/gilad/briana/genome_anotation_data/genome_200_wind_fix2.saf -F 'SAF' -o /project2/gilad/briana/threeprimeseq/data/cov_200/${describer}_FC200.cov.bed $1
ERROR: invalid parameter:
I will need to create a wrapper to run this for all of the files.
#!/bin/bash
#SBATCH --job-name=w_cov200
#SBATCH --time=8:00:00
#SBATCH --output=w_cov200.out
#SBATCH --error=w_cov2--.err
#SBATCH --partition=broadwl
#SBATCH --mem=8G
#SBATCH --mail-type=END
for i in $(ls /project2/gilad/briana/threeprimeseq/data/bed_sort/); do
sbatch cov200.sh /project2/gilad/briana/threeprimeseq/data/bed_sort/$i
done
sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] workflowr_1.0.1 Rcpp_0.12.15 digest_0.6.14
[4] rprojroot_1.3-2 R.methodsS3_1.7.1 backports_1.1.2
[7] git2r_0.21.0 magrittr_1.5 evaluate_0.10.1
[10] stringi_1.1.6 whisker_0.3-2 R.oo_1.22.0
[13] R.utils_2.6.0 rmarkdown_1.8.5 tools_3.4.2
[16] stringr_1.2.0 yaml_2.1.16 compiler_3.4.2
[19] htmltools_0.3.6 knitr_1.18
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