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Last updated: 2019-01-17

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Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    data/.DS_Store
    Ignored:    output/.DS_Store

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    Untracked:  KalistoAbundance18486.txt
    Untracked:  analysis/DirectionapaQTL.Rmd
    Untracked:  analysis/EvaleQTLs.Rmd
    Untracked:  analysis/PreAshExplore.Rmd
    Untracked:  analysis/YL_QTL_test.Rmd
    Untracked:  analysis/ncbiRefSeq_sm.sort.mRNA.bed
    Untracked:  analysis/snake.config.notes.Rmd
    Untracked:  analysis/verifyBAM.Rmd
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    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/bedgraph_peaks/
    Untracked:  data/bin200.5.T.nuccov.bed
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    Untracked:  data/clean_peaks/
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    Untracked:  data/comb_map_stats_39ind.csv
    Untracked:  data/combined_reads_mapped_three_prime_seq.csv
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    Untracked:  data/ensemble_to_genename.txt
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    Untracked:  data/explainProtVar/
    Untracked:  data/filtered_APApeaks_merged_allchrom_refseqTrans.closest2End.bed
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    Untracked:  data/first50lines_closest.txt
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    Untracked:  data/joined
    Untracked:  data/leafcutter/
    Untracked:  data/merged_combined_YL-SP-threeprimeseq.bg
    Untracked:  data/mol_overlap/
    Untracked:  data/mol_pheno/
    Untracked:  data/nom_QTL/
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    Untracked:  data/other_qtls/
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Unstaged changes:
    Modified:   analysis/28ind.peak.explore.Rmd
    Modified:   analysis/CompareLianoglouData.Rmd
    Modified:   analysis/NewPeakPostMP.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/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.

Expand here to see past versions:

File	Version	Author	Date	Message
Rmd	7eaae54	Briana Mittleman	2019-01-17	select peaks to use in deeptools plot
html	a5d48fd	Briana Mittleman	2019-01-16	Build site.
Rmd	6aa94e4	Briana Mittleman	2019-01-16	plots for 5% usage
html	e088c55	Briana Mittleman	2019-01-14	Build site.
Rmd	6bc9243	Briana Mittleman	2019-01-14	evaluate clean reads, make new file for misprime filter
html	580e244	Briana Mittleman	2019-01-11	Build site.
Rmd	42fcbdd	Briana Mittleman	2019-01-11	initialize mispriming approach file
html	4d935ce	Briana Mittleman	2019-01-03	Build site.
Rmd	c3b3bbb	Briana Mittleman	2019-01-03	start covariate correlation with pc analysis
html	785b821	Briana Mittleman	2018-12-20	Build site.
Rmd	d99a6f3	Briana Mittleman	2018-12-20	initializa comparison analysis
html	6da90e9	Briana Mittleman	2018-12-11	Build site.
html	1b3647a	Briana Mittleman	2018-12-10	Build site.
Rmd	28e2214	Briana Mittleman	2018-12-10	start qtls by included PC analysis
html	cdfa5b2	Briana Mittleman	2018-12-05	Build site.
Rmd	655b582	Briana Mittleman	2018-12-05	PCA with batch and read count
html	210b58b	Briana Mittleman	2018-11-29	Build site.
Rmd	413c8fd	Briana Mittleman	2018-11-29	add filter QTL analysis and start explain pqtl
html	813a500	Briana Mittleman	2018-11-15	Build site.
Rmd	23c62c9	Briana Mittleman	2018-11-15	add locus zoom initial analysis
html	e5b4d6a	Briana Mittleman	2018-11-15	Build site.
Rmd	a9d3372	Briana Mittleman	2018-11-15	fix gwas bullet
html	24821f2	Briana Mittleman	2018-11-12	Build site.
html	2ec5ffd	Briana Mittleman	2018-11-07	Build site.
Rmd	962e39b	Briana Mittleman	2018-11-07	move chromhmm analysis to its own analysis
html	3de0848	Briana Mittleman	2018-11-06	Build site.
Rmd	b5f744f	Briana Mittleman	2018-11-06	initiate flash2mash
html	d01545f	Briana Mittleman	2018-10-30	Build site.
Rmd	9c9486d	Briana Mittleman	2018-10-30	add genoem tracks code
html	0428c8c	Briana Mittleman	2018-10-29	Build site.
Rmd	42d0e3d	Briana Mittleman	2018-10-29	add gwas overlap to index
html	de860f0	Briana Mittleman	2018-10-24	Build site.
Rmd	96a97f4	Briana Mittleman	2018-10-24	add nuclear characterization
html	5649809	Briana Mittleman	2018-10-22	Build site.
Rmd	c8dbaf0	Briana Mittleman	2018-10-22	add apa prot rna overlap
html	eb02fbc	Briana Mittleman	2018-10-11	Build site.
Rmd	f819c8e	Briana Mittleman	2018-10-11	add distance metric analsis total apaQTL
html	a7e5fa2	Briana Mittleman	2018-10-11	Build site.
Rmd	1e7fbbb	Briana Mittleman	2018-10-11	update format
html	729c084	Briana Mittleman	2018-10-11	Build site.
Rmd	89f119a	Briana Mittleman	2018-10-11	update format
html	22aa087	Briana Mittleman	2018-10-08	Build site.
Rmd	11f9dfa	Briana Mittleman	2018-10-08	overlap molQTL opp dir
html	077ed60	Briana Mittleman	2018-10-08	Build site.
html	7369f8e	Briana Mittleman	2018-10-02	Build site.
Rmd	f66679b	Briana Mittleman	2018-10-02	overlap plots at peak level
html	2e0d959	Briana Mittleman	2018-10-01	Build site.
Rmd	9d6ee03	Briana Mittleman	2018-10-01	add 4su plots
html	da0f70e	Briana Mittleman	2018-10-01	Build site.
Rmd	fecb046	Briana Mittleman	2018-10-01	fix overlapfile
html	ac983db	Briana Mittleman	2018-10-01	Build site.
Rmd	35142fb	Briana Mittleman	2018-10-01	overlap QTL plots
html	149d033	Briana Mittleman	2018-09-26	Build site.
html	aaed5fd	Briana Mittleman	2018-09-26	Build site.
Rmd	eda266e	Briana Mittleman	2018-09-26	test peak to gene transcript dist
html	47cd4bf	Briana Mittleman	2018-09-26	Build site.
html	b1bcf99	Briana Mittleman	2018-09-25	Build site.
html	d3bb287	Briana Mittleman	2018-09-24	Build site.
Rmd	f7934ce	Briana Mittleman	2018-09-24	wflow_publish(c(“index.Rmd”, “39indQC.Rmd”))
html	f92a58f	Briana Mittleman	2018-09-06	Build site.
Rmd	46b7343	Briana Mittleman	2018-09-06	add overlap analysis with code to subset
html	b4bda1b	Briana Mittleman	2018-08-30	Build site.
html	e000583	Briana Mittleman	2018-08-30	Build site.
Rmd	a5f5276	Briana Mittleman	2018-08-30	initialize diff iso pipeline
html	c6dc97b	brimittleman	2018-08-28	Build site.
html	5564e25	brimittleman	2018-08-20	Build site.
Rmd	6b1b51c	brimittleman	2018-08-20	start qtl analsis, add to index
html	c67380e	brimittleman	2018-08-14	Build site.
html	38bfbaf	brimittleman	2018-08-09	Build site.
Rmd	03761cb	brimittleman	2018-08-09	start peak explore analysis for 54 libraries
html	e5a8da6	Briana Mittleman	2018-07-30	Build site.
Rmd	422a428	Briana Mittleman	2018-07-30	add peak cove pipeline and combined lane qc
html	0398fdb	Briana Mittleman	2018-07-25	Build site.
Rmd	2d41f11	Briana Mittleman	2018-07-25	add expand smash to index
html	3a5a8fe	Briana Mittleman	2018-07-25	Build site.
html	a34f9c1	Briana Mittleman	2018-07-17	Build site.
Rmd	ca9cee9	Briana Mittleman	2018-07-17	add smash test to index
html	c3ca148	Briana Mittleman	2018-07-17	Build site.
html	dc4a51a	Briana Mittleman	2018-07-16	Build site.
Rmd	4fede84	Briana Mittleman	2018-07-16	add eval brain analysis
html	cfc8f43	Briana Mittleman	2018-07-13	Build site.
Rmd	4a84769	Briana Mittleman	2018-07-13	add analysis for coparing coverage of RNAseq and 3’ seq
html	210cd2b	Briana Mittleman	2018-07-05	Build site.
Rmd	8b622c3	Briana Mittleman	2018-07-05	add denovo to index
html	ee777df	Briana Mittleman	2018-06-26	Build site.
Rmd	789d8ef	Briana Mittleman	2018-06-26	start test macs analysis. download package
html	30b415e	Briana Mittleman	2018-06-19	Build site.
html	08b5934	Briana Mittleman	2018-06-13	Build site.
Rmd	642faf0	Briana Mittleman	2018-06-13	start PAS enrichment analysis
html	4ef7d85	Briana Mittleman	2018-06-11	Build site.
Rmd	03c7b14	Briana Mittleman	2018-06-11	start A analysis
html	062808d	Briana Mittleman	2018-06-07	Build site.
html	86cfd9f	Briana Mittleman	2018-06-06	Build site.
Rmd	a19683c	Briana Mittleman	2018-06-06	start dif isoform analysis
html	710cf6a	Briana Mittleman	2018-05-29	Build site.
Rmd	d58bc13	Briana Mittleman	2018-05-29	start 200 bp analysis
html	96ecbb1	Briana Mittleman	2018-05-26	Build site.
Rmd	2076ce9	Briana Mittleman	2018-05-26	initial commit, gene level analysis
html	b5cdd59	Briana Mittleman	2018-05-26	Build site.
Rmd	9a49459	Briana Mittleman	2018-05-26	start map qc analysis
html	924952b	Briana Mittleman	2018-05-09	Build site.
Rmd	f8ce0fc	Briana Mittleman	2018-05-09	Update to 1.0
html	f8ce0fc	Briana Mittleman	2018-05-09	Update to 1.0
html	3dd80ef	Briana Mittleman	2018-05-08	Build site.
Rmd	519447d	Briana Mittleman	2018-05-08	Add total.nuc.rnaseq analysis
html	889c9c6	Briana Mittleman	2018-05-02	Build site.
html	9d196cf	Briana Mittleman	2018-05-02	Build site.
html	972ef3e	Briana Mittleman	2018-05-02	Build site.
Rmd	6cc5321	Briana Mittleman	2018-05-02	add home page information
html	e12dd6c	Briana Mittleman	2018-05-01	Build site.
Rmd	0e95115	Briana Mittleman	2018-05-01	add home page information
html	4c26d4c	Briana Mittleman	2018-05-01	Build site.
Rmd	539892a	Briana Mittleman	2018-05-01	Start workflowr project.

Briana Mittleman

This is the site I will use for my human 3’ seq project. I will have my workflow and analysis here. The three prime seq protocol I am using is Lexogen, QuantSeq 3’ mRNA-Seq library kit. The first analysis will be on the total and nucleic fractions of the LCL used in the net-seq analysis found at https://brimittleman.github.io/Net-seq/

Initial analysis on RNA seq of nuclear and total fractions:

Initial data QC

Initial analysis on first 32 3’ seq libraries:

Explore and filter mis-primming:

Peak calling:

Peak coverage/Nominal QTLs/Diff iso:

Rerun analysis opp strand:

Rerun QTL analysis with off strand

Evaluate and learn from QTLs:

Overlap QTLs with other molecular QTLs

Analysis for all 39 indivduals:

Molecular QTL analysis and Overlap:

Until now I have been focusing on way to develop the story for the paper. The next steps will be to systematically understand the data in order to filter to high quality data to use in the final analysis.

This reproducible R Markdown analysis was created with workflowr 1.1.1