Last updated: 2019-02-07
workflowr checks: (Click a bullet for more information)Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
set.seed(12345)
The command set.seed(12345)
was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
wflow_publish
or wflow_git_commit
). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Ignored files:
Ignored: .DS_Store
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: data/.DS_Store
Ignored: data/perm_QTL_trans_noMP_5percov/
Ignored: output/.DS_Store
Untracked files:
Untracked: KalistoAbundance18486.txt
Untracked: analysis/4suDataIGV.Rmd
Untracked: analysis/DirectionapaQTL.Rmd
Untracked: analysis/EvaleQTLs.Rmd
Untracked: analysis/YL_QTL_test.Rmd
Untracked: analysis/ncbiRefSeq_sm.sort.mRNA.bed
Untracked: analysis/snake.config.notes.Rmd
Untracked: analysis/verifyBAM.Rmd
Untracked: analysis/verifybam_dubs.Rmd
Untracked: code/PeaksToCoverPerReads.py
Untracked: code/strober_pc_pve_heatmap_func.R
Untracked: data/18486.genecov.txt
Untracked: data/APApeaksYL.total.inbrain.bed
Untracked: data/ApaQTLs/
Untracked: data/ChromHmmOverlap/
Untracked: data/DistTXN2Peak_genelocAnno/
Untracked: data/GM12878.chromHMM.bed
Untracked: data/GM12878.chromHMM.txt
Untracked: data/LianoglouLCL/
Untracked: data/LocusZoom/
Untracked: data/NuclearApaQTLs.txt
Untracked: data/PeakCounts/
Untracked: data/PeakCounts_noMP_5perc/
Untracked: data/PeakCounts_noMP_genelocanno/
Untracked: data/PeakUsage/
Untracked: data/PeakUsage_noMP/
Untracked: data/PeakUsage_noMP_GeneLocAnno/
Untracked: data/PeaksUsed/
Untracked: data/PeaksUsed_noMP_5percCov/
Untracked: data/RNAkalisto/
Untracked: data/RefSeq_annotations/
Untracked: data/TotalApaQTLs.txt
Untracked: data/Totalpeaks_filtered_clean.bed
Untracked: data/UnderstandPeaksQC/
Untracked: data/YL-SP-18486-T-combined-genecov.txt
Untracked: data/YL-SP-18486-T_S9_R1_001-genecov.txt
Untracked: data/YL_QTL_test/
Untracked: data/apaExamp/
Untracked: data/apaQTL_examp_noMP/
Untracked: data/bedgraph_peaks/
Untracked: data/bin200.5.T.nuccov.bed
Untracked: data/bin200.Anuccov.bed
Untracked: data/bin200.nuccov.bed
Untracked: data/clean_peaks/
Untracked: data/comb_map_stats.csv
Untracked: data/comb_map_stats.xlsx
Untracked: data/comb_map_stats_39ind.csv
Untracked: data/combined_reads_mapped_three_prime_seq.csv
Untracked: data/diff_iso_GeneLocAnno/
Untracked: data/diff_iso_proc/
Untracked: data/diff_iso_trans/
Untracked: data/ensemble_to_genename.txt
Untracked: data/example_gene_peakQuant/
Untracked: data/explainProtVar/
Untracked: data/filtPeakOppstrand_cov_noMP_GeneLocAnno_5perc/
Untracked: data/filtered_APApeaks_merged_allchrom_refseqTrans.closest2End.bed
Untracked: data/filtered_APApeaks_merged_allchrom_refseqTrans.closest2End.noties.bed
Untracked: data/first50lines_closest.txt
Untracked: data/gencov.test.csv
Untracked: data/gencov.test.txt
Untracked: data/gencov_zero.test.csv
Untracked: data/gencov_zero.test.txt
Untracked: data/gene_cov/
Untracked: data/joined
Untracked: data/leafcutter/
Untracked: data/merged_combined_YL-SP-threeprimeseq.bg
Untracked: data/molPheno_noMP/
Untracked: data/mol_overlap/
Untracked: data/mol_pheno/
Untracked: data/nom_QTL/
Untracked: data/nom_QTL_opp/
Untracked: data/nom_QTL_trans/
Untracked: data/nuc6up/
Untracked: data/nuc_10up/
Untracked: data/other_qtls/
Untracked: data/pQTL_otherphen/
Untracked: data/peakPerRefSeqGene/
Untracked: data/perm_QTL/
Untracked: data/perm_QTL_GeneLocAnno_noMP_5percov/
Untracked: data/perm_QTL_GeneLocAnno_noMP_5percov_3UTR/
Untracked: data/perm_QTL_opp/
Untracked: data/perm_QTL_trans/
Untracked: data/perm_QTL_trans_filt/
Untracked: data/protAndAPAAndExplmRes.Rda
Untracked: data/protAndAPAlmRes.Rda
Untracked: data/protAndExpressionlmRes.Rda
Untracked: data/reads_mapped_three_prime_seq.csv
Untracked: data/smash.cov.results.bed
Untracked: data/smash.cov.results.csv
Untracked: data/smash.cov.results.txt
Untracked: data/smash_testregion/
Untracked: data/ssFC200.cov.bed
Untracked: data/temp.file1
Untracked: data/temp.file2
Untracked: data/temp.gencov.test.txt
Untracked: data/temp.gencov_zero.test.txt
Untracked: data/threePrimeSeqMetaData.csv
Untracked: data/threePrimeSeqMetaData55Ind.txt
Untracked: data/threePrimeSeqMetaData55Ind.xlsx
Untracked: output/picard/
Untracked: output/plots/
Untracked: output/qual.fig2.pdf
Unstaged changes:
Modified: analysis/28ind.peak.explore.Rmd
Modified: analysis/CompareLianoglouData.Rmd
Modified: analysis/apaQTLoverlapGWAS.Rmd
Modified: analysis/cleanupdtseq.internalpriming.Rmd
Modified: analysis/coloc_apaQTLs_protQTLs.Rmd
Modified: analysis/dif.iso.usage.leafcutter.Rmd
Modified: analysis/diff_iso_pipeline.Rmd
Modified: analysis/explainpQTLs.Rmd
Modified: analysis/explore.filters.Rmd
Modified: analysis/flash2mash.Rmd
Modified: analysis/mispriming_approach.Rmd
Modified: analysis/overlapMolQTL.Rmd
Modified: analysis/overlapMolQTL.opposite.Rmd
Modified: analysis/overlap_qtls.Rmd
Modified: analysis/peakOverlap_oppstrand.Rmd
Modified: analysis/peakQCPPlots.Rmd
Modified: analysis/pheno.leaf.comb.Rmd
Modified: analysis/pipeline_55Ind.Rmd
Modified: analysis/swarmPlots_QTLs.Rmd
Modified: analysis/test.max2.Rmd
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 |
---|---|---|---|---|
Rmd | 3fea644 | Briana Mittleman | 2019-02-07 | add accountmapbias |
We are worried there amy be false positives in the QTL analysis if the QTL is in the read and the snp leads to a mapping bias for the data. I can account for this using WASP.
I have an example script from Yang:
/project2/yangili1/yangili/TCGA_pipe/script_process.sh
STAR2.6 --genomeDir /project2/yangili1/RNAseq_pipeline/index/GRCh37/STAR_hg19 --readFilesIn $inFile\_1.fastq $inFile\_2.fastq --outSAMstrandField intronMotif --outFileNamePrefix $outFile. --outSAMtype BAM Unsorted --varVCFfile $vcfFile --waspOutputMode SAMtag --outSAMattributes vA vG
First I need to find my star indexed genome:
*/project2/gilad/briana/genome_anotation_data/star_genome
Next I need my VCF file:
runStarwWASP.sh
#!/bin/bash
#SBATCH --job-name=runStarwWASP
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=runStarwWASP.out
#SBATCH --error=runStarwWASP.err
#SBATCH --partition=bigmem2
#SBATCH --mem=100G
#SBATCH --mail-type=END
module load Anaconda3
source activate three-prime-env
in=$1
out=$2
STAR --runThreadN 4 --genomeDir /project2/gilad/briana/genome_anotation_data/star_genome --readFilesIn $1 --outSAMstrandField intronMotif --outFileNamePrefix /project2/gilad/briana/threeprimeseq/data/STAR_bam_WASP/$2.combined.STARwWASP.bam --outSAMtype BAM Unsorted --varVCFfile /project2/gilad/briana/YRI_geno_hg19/allChrom.dose.filt.vcf --waspOutputMode SAMtag --outSAMattributes vA vG
test_runStartwWASP.sh
#!/bin/bash
#SBATCH --job-name=test_runStarwWASP
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=test_runStarwWASP.out
#SBATCH --error=test_runStarwWASP.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END
module load Anaconda3
source activate three-prime-env
i=/project2/gilad/briana/threeprimeseq/data/fastq/YL-SP-19239-T-combined.fastq
describer=$(echo ${i} | sed -e 's/.*YL-SP-//' | sed -e "s/combined.fastq//")
sbatch runStarwWASP.sh $i $describer
Wraper:
wrap_runStarwWASP.sh
#!/bin/bash
#SBATCH --job-name=wrap_runStarwWASP
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=wrap_runStarwWASP.out
#SBATCH --error=wrap_runStarwWASP.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END
module load Anaconda3
source activate three-prime-env
for i in $(ls /project2/gilad/briana/threeprimeseq/data/fastq/*);do
describer=$(echo ${i} | sed -e 's/.*YL-SP-//' | sed -e "s/combined.fastq//")
sbatch runStarwWASP.sh $i $describer
done
Quota reached at 19193N for jobs- create a wrap2
wrap_runStarwWASP2.sh
#!/bin/bash
#SBATCH --job-name=wrap_runStarwWASP2
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=wrap_runStarwWASP2.out
#SBATCH --error=wrap_runStarwWASP2.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END
module load Anaconda3
source activate three-prime-env
for i in $(ls /project2/gilad/briana/threeprimeseq/data/fastq/YL-SP-192*); do
describer=$(echo ${i} | sed -e 's/.*YL-SP-//' | sed -e "s/combined.fastq//")
sbatch runStarwWASP.sh $i $describer
done
Sort and index these files.
SortIndexStarwWASP.sh
#!/bin/bash
#SBATCH --job-name=SortIndexStarwWASP
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=SortIndexStarwWASP.out
#SBATCH --error=SortIndexStarwWASP.err
#SBATCH --partition=broadwl
#SBATCH --mem=36G
#SBATCH --mail-type=END
module load Anaconda3
source activate three-prime-env
describer=$1
samtools sort /project2/gilad/briana/threeprimeseq/data/STAR_bam_WASP/${describer}combined.STARwWASP.bamAligned.out.bam > /project2/gilad/briana/threeprimeseq/data/STAR_bam_WASP_sort/${describer}combined.STARwWASP.bamAligned.sort.bam
samtools index /project2/gilad/briana/threeprimeseq/data/STAR_bam_WASP_sort/${describer}combined.STARwWASP.bamAligned.sort.bam
wrap_SortIndexStarwWASP.sh
#!/bin/bash
#SBATCH --job-name=wrap_SortIndexStarwWASP
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=wrap_SortIndexStarwWASP.out
#SBATCH --error=wrap_SortIndexStarwWASP.err
#SBATCH --partition=broadwl
#SBATCH --mem=36G
#SBATCH --mail-type=END
module load Anaconda3
source activate three-prime-env
for i in $(ls /project2/gilad/briana/threeprimeseq/data/STAR_bam_WASP/*STARwWASP.bamAligned.out.bam)
describer=$(echo ${i} | sed -e 's/.*YL-SP-//' | sed -e "s/combined.STARwWASP.bamAligned.out.bam//")
sbatch SortIndexStarwWASP.sh $describer
done
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
This reproducible R Markdown analysis was created with workflowr 1.1.1