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ChIP-seq improvements #460

Merged
merged 20 commits into from
Sep 14, 2020
Merged

ChIP-seq improvements #460

merged 20 commits into from
Sep 14, 2020

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tovahmarkowitz
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This pull request involves the following changes:

  1. FRiP visualization improvements (now uses R) and pdf file format. Also improved speed of FRiP processing by allowing for more parallelization.
  2. Improved mapQ filtering for PE data using Vishal's python script (Fix error with PE duplicate removal. Incorporate Vishal's code. #457 )
  3. Using picard to calculate insert sizes for PE data (Calculate actual mean fragment length for PE data. Use for sicer PE. #458 )
  4. Using median insert size for peak calling using sicer for PE data
  5. minor bug fixes

tovahmarkowitz and others added 20 commits September 17, 2019 12:45
@tovahmarkowitz
improving estimated fragment length
1d963fb
@tovahmarkowitz
gerge branch 'activeDev' of https://github.com/CCBR/Pipeliner into ac…
27f48f0 
…tiveDev
@tovahmarkowitz
est fraglen; diffbind
e34f537
@tovahmarkowitz
Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into ac…
9939ce6 
…tiveDev
@tovahmarkowitz
DiffBind and cleanup
88bb874
@tovahmarkowitz
Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into ac…
8846dcb 
…tiveDev
@tovahmarkowitz
ppqt changes
f93311c
@tovahmarkowitz
Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into ac…
7dc7ceb 
…tiveDev
@tovahmarkowitz
ppqt improvements and a few other details
6dc7200
@wong-nw @skchronicles
@mtandon09 @jlac
scRNASeq changes Feb 2020 (#438)
57c2e14 
* scRNASeq changes Feb 2020

* March updates

* Merging activeDev for v4.0.1 release (#444)

* Fix sequenza error

* Scrnaseq (#437)

Scrnaseq: miRNA-seq changes and scRNA-seq changes

* Symlink counts matrix if "counts/" exists in users rawdata directory

* Dectect if users is starting from a raw counts matrix

* Updating pop-up box dialogue after detection of new counts matrix filetype

* Find differential expression metadata in "/path/to/rawdata/counts/"

* Readability: checking for counts matrix outside conditional statement

* Adding "--alignEndsProtrude 10 ConcordantPair --peOverlapNbasesMin 10" to the first and second pass of STAR

* Explicitly loading 'python/2.7': default version of python changing to '3.7'

Co-authored-by: Mayank  Tandon <[email protected]>
Co-authored-by: wong-nw <[email protected]>
Co-authored-by: jlac <[email protected]>

Co-authored-by: Skyler Kuhn <[email protected]>
Co-authored-by: Mayank  Tandon <[email protected]>
Co-authored-by: jlac <[email protected]>
Co-authored-by: skchronicles <[email protected]>
@tovahmarkowitz
improving ppqt, diffbind, frip, and jaccard
c7f40cc
@tovahmarkowitz
fixing merge issue
26d1d7b
@tovahmarkowitz
updating to most recent version of activeDev
1e958f2
@tovahmarkowitz
fixed the InitialChIPseqQC.snakefile conflict
c2435f7
@tovahmarkowitz
fastqc bug fixed
326ab3c
@tovahmarkowitz
more memory for BWA in ChIP-seq pipeline
1a128a9
@tovahmarkowitz
reverting ngsqc_plot to a version that functions
2071cea
@tovahmarkowitz
Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into ac…
a9e980b 
…tiveDev
@tovahmarkowitz
fixing FRiP
b7d1c65
@tovahmarkowitz
improved ChIP-seq PE and bug fixes
ed3be62
@skchronicles
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Thanks @tovahmarkowitz for submitting the PR, everything looks good!

@skchronicles skchronicles merged commit 12e332f into CCBR:activeDev Sep 14, 2020
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@skchronicles skchronicles Awaiting requested review from skchronicles

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@tovahmarkowitz @skchronicles @wong-nw