Last updated: 2018-10-08

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      Modified:   analysis/28ind.peak.explore.Rmd
      Modified:   analysis/39indQC.Rmd
      Modified:   analysis/PeakToGeneAssignment.Rmd
      Modified:   analysis/cleanupdtseq.internalpriming.Rmd
      Modified:   analysis/dif.iso.usage.leafcutter.Rmd
      Modified:   analysis/diff_iso_pipeline.Rmd
      Modified:   analysis/explore.filters.Rmd
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      Modified:   code/Snakefile
  
  

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Expand here to see past versions:

File	Version	Author	Date	Message
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.

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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:

• Initial mapping QC
• Initial gene leve QC
  
• Compare coverage in Three prime seq to RNAseq
  
• Coverage in 200bp bins
  
• Differential isoform usage between fractions
  
• Explore filter cuttoffs
  
• Enrichment at PAS
  
• Second Lane data

Explore and filter mis-primming:

• Look at number of As in bins
  
• Create script to filter mapped A’s
  
• Test cleanUpdTSeq for calling internal priming
  
• Pipeline to create peaks and clean them

Peak calling:

• Testing macs2 on 3’seq data
  
• Call peak regions de-novo
• Compare peaks in Derti Brain set
  
• Test SMASH smoothing
  
• Expand SMASH analysis for use on midway
  
• Data Processing Figure design

Peak coverage/Nominal QTLs/Diff iso:

• Start evaluating peak quantificaiton
  
• Prepare the data for leafcutter QTL calling
• Call nominal QTLs
  
• Differential Isoform pipeline

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:

• Read and peak QC plots

• APAqtl for full ind set

• Rethink Peak to Gene assignment

• Condition Total and Nuclear QTLs on each other

Molecular QTL analysis and Overlap:

• Rerun molecular QTLs

• Make overlap QTL plots

• Plot top apaQTLs in other phenotypes

• Overlap QTLs starting with APAqtls

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