Last updated: 2019-02-01
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Unstaged changes:
Modified: analysis/28ind.peak.explore.Rmd
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Modified: analysis/understandPeaks.Rmd
Modified: code/Snakefile
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes. File | Version | Author | Date | Message |
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Rmd | 957a0ee | Briana Mittleman | 2019-02-01 | initiate 55 ind pipeline |
First I need to move the duplicate files to a different dir. data/Replicates
YL-SP-18499-N-batch4.combined-sort.bed YL-SP-18499-T-batch4.combined-sort.bed
YL-SP-18912-N-batch4.combined-sort.bed YL-SP-18912-T-batch4.combined-sort.bed
YL-SP-19093-N-batch4.combined-sort.bed YL-SP-19093-T-batch4.combined-sort.bed
YL-SP-19140-N-batch4.combined-sort.bed YL-SP-19140-T-batch4.combined-sort.bed
-Bedsort
-sort
Remove 18497-N (18499) 18497-T (18499) 18500-N (18501) 18500-T (18501)
Mispriming
- Get 10 basepairs upstream: wrap_Upstream10Bases.sh
- Find sequence for these regions: Nuc10BasesUp.sh
- find which are bad run_filterMissprimingInNuc10.sh - filter bed file run_filterSortBedbyCleanedBed.sh - sort clean bed file sort_filterSortBedbyCleanedBed.sh - filter bam files wrap_filterBamforMP.pysam2.sh
- sort and index clean bam SortIndexBam_noMP.sh - merge clean bam files mergeBamFiles_noMP.sh
- sort and index merged SortIndexMergedBam_noMP.sh
- create BW mergedBam2Bedgraph.sh
- make it a coverage file run_bgtocov_noMP.sh - call peaks run_callPeaksYL_noMP.sh
- filter peaks - cat /project2/gilad/briana/threeprimeseq/data/mergedPeaks_noMP/*.bed > /project2/gilad/briana/threeprimeseq/data/mergedPeaks_noMP/APApeaks_merged_allchrom_noMP.bed
- make SAF file bed2saf_noMP.py - run feature counts peak_fc_noMP.sh - filter peaks run_filter_peaks_noMP.sh
- name peaks
x = wc -l /project2/gilad/briana/threeprimeseq/data/mergedPeaks_noMP_filtered/Filtered_APApeaks_merged_allchrom_noMP.bed
seq 1 x > peak.num.txt
sort -k1,1 -k2,2n Filtered_APApeaks_merged_allchrom_noMP.bed > Filtered_APApeaks_merged_allchrom_noMP.sort.bed
paste /project2/gilad/briana/threeprimeseq/data/mergedPeaks_noMP_filtered/Filtered_APApeaks_merged_allchrom_noMP.sort.bed peak.num.txt | column -s $'\t' -t > temp
awk '{print $1 "\t" $2 "\t" $3 "\t" $7 "\t" $4 "\t" $5 "\t" $6}' temp > /project2/gilad/briana/threeprimeseq/data/mergedPeaks_noMP_filtered/Filtered_APApeaks_merged_allchrom_noMP.sort.named.bed
#cut the chr
sed 's/^chr//' /project2/gilad/briana/threeprimeseq/data/mergedPeaks_noMP_filtered/Filtered_APApeaks_merged_allchrom_noMP.sort.named.bed > /project2/gilad/briana/threeprimeseq/data/mergedPeaks_noMP_filtered/Filtered_APApeaks_merged_allchrom_noMP.sort.named.noCHR.bed
Make script to filter 5%
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.14.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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_1.1.1 Rcpp_0.12.19 digest_0.6.17
[4] rprojroot_1.3-2 R.methodsS3_1.7.1 backports_1.1.2
[7] git2r_0.23.0 magrittr_1.5 evaluate_0.11
[10] stringi_1.2.4 whisker_0.3-2 R.oo_1.22.0
[13] R.utils_2.7.0 rmarkdown_1.10 tools_3.5.1
[16] stringr_1.3.1 yaml_2.2.0 compiler_3.5.1
[19] htmltools_0.3.6 knitr_1.20
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