Last updated: 2019-03-26
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Knit directory: threeprimeseq/analysis/
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Modified: analysis/unexplainedeQTL_analysis.Rmd
Modified: code/Snakefile
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | a6b0fe4 | Briana Mittleman | 2019-03-20 | Build site. |
| Rmd | 54168fd | Briana Mittleman | 2019-03-20 | add histone mod analysis |
| html | 9aa1003 | Briana Mittleman | 2019-03-19 | Build site. |
| Rmd | d924da6 | Briana Mittleman | 2019-03-19 | add ctcf analysis |
| html | 1283669 | Briana Mittleman | 2019-03-15 | Build site. |
| Rmd | 5d6ac93 | Briana Mittleman | 2019-03-15 | add decay analysis |
| html | f696384 | Briana Mittleman | 2019-03-13 | Build site. |
| Rmd | 01c22a6 | Briana Mittleman | 2019-03-13 | eQTL and unexp eQTL res |
| html | f88b41f | Briana Mittleman | 2019-03-13 | Build site. |
| Rmd | f9e94cf | Briana Mittleman | 2019-03-13 | add net seq analysis |
| html | 4b2da32 | Briana Mittleman | 2019-03-12 | Build site. |
| html | 8a6b54e | Briana Mittleman | 2019-03-11 | Build site. |
| Rmd | 8871122 | Briana Mittleman | 2019-03-11 | subset to x% |
| html | 9d234b6 | Briana Mittleman | 2019-03-09 | Build site. |
| html | 55a488c | Briana Mittleman | 2019-03-09 | Build site. |
| Rmd | ea54d47 | Briana Mittleman | 2019-03-09 | add new GWAS overlap |
| html | ba63ea2 | Briana Mittleman | 2019-03-06 | Build site. |
| Rmd | c200503 | Briana Mittleman | 2019-03-06 | add signal site loc analysis |
| html | 08ca500 | Briana Mittleman | 2019-03-04 | Build site. |
| Rmd | d5d0809 | Briana Mittleman | 2019-03-04 | add analysis |
| html | 901e191 | Briana Mittleman | 2019-03-02 | Build site. |
| Rmd | a96297c | Briana Mittleman | 2019-03-02 | add signal site enrich analysis |
| html | 19ad929 | Briana Mittleman | 2019-03-01 | Build site. |
| Rmd | f812272 | Briana Mittleman | 2019-03-01 | add erna and rep element analysis |
| html | a259bd9 | Briana Mittleman | 2019-02-27 | Build site. |
| Rmd | eb1a05c | Briana Mittleman | 2019-02-27 | add pacbio analysis |
| html | b74a969 | Briana Mittleman | 2019-02-25 | Build site. |
| Rmd | 2336f87 | Briana Mittleman | 2019-02-25 | add unexplained QTL analysis |
| html | 194c94d | Briana Mittleman | 2019-02-19 | Build site. |
| Rmd | 41500e4 | Briana Mittleman | 2019-02-19 | add prot and rna |
| html | cefce8b | Briana Mittleman | 2019-02-19 | Build site. |
| html | beb0d71 | Briana Mittleman | 2019-02-18 | Build site. |
| Rmd | 3c1f049 | Briana Mittleman | 2019-02-18 | add gwas overlap |
| html | 4ea438e | Briana Mittleman | 2019-02-18 | Build site. |
| Rmd | bcb2f86 | Briana Mittleman | 2019-02-18 | add qtl by per and diff iso |
| html | 879be33 | Briana Mittleman | 2019-02-16 | Build site. |
| Rmd | f8c76ea | Briana Mittleman | 2019-02-16 | move peak QC plots |
| html | c2c77b6 | Briana Mittleman | 2019-02-15 | Build site. |
| Rmd | b7a0e32 | Briana Mittleman | 2019-02-15 | add window size qtl analysis |
| html | 4f17cca | Briana Mittleman | 2019-02-15 | Build site. |
| html | b8cfd6f | Briana Mittleman | 2019-02-07 | Build site. |
| Rmd | 3fea644 | Briana Mittleman | 2019-02-07 | add accountmapbias |
| html | 450b389 | Briana Mittleman | 2019-02-06 | Build site. |
| Rmd | 6bac9f9 | Briana Mittleman | 2019-02-06 | add distance plots for QC on APAqtls |
| html | cc6b1ee | Briana Mittleman | 2019-02-05 | Build site. |
| html | 3445a3b | Briana Mittleman | 2019-02-01 | Build site. |
| Rmd | 957a0ee | Briana Mittleman | 2019-02-01 | initiate 55 ind pipeline |
| html | a97adbc | Briana Mittleman | 2019-01-28 | Build site. |
| Rmd | a2911ff | Briana Mittleman | 2019-01-28 | start analysis for new gene peak assignemnt |
| html | 7120162 | Briana Mittleman | 2019-01-24 | Build site. |
| Rmd | 9df8d7e | Briana Mittleman | 2019-01-24 | add linear model code with res for stephens lab |
| html | aefc330 | Briana Mittleman | 2019-01-22 | Build site. |
| Rmd | fd184be | Briana Mittleman | 2019-01-22 | add code for leafcutter on processed |
| html | 6e22653 | Briana Mittleman | 2019-01-17 | Build site. |
| 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. |
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| 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/
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.
In the previous sections (specifically here) I reran some QC and the QTL analysis with the filtered and clean data. Here I want to look at some of the other analysis with the processed data.
I now have 55 individuals. I am going to call peaks and QTLs in this data.