encode3-curation

This is my collection of IPython notebooks to document some of the work I've done to try and curate the Wold Lab's data submissions to the ENCODE-DCC.

Originally I just started sharing it so I could show my work to our super data wrangler.

However I then started writing some notebooks that might be considered useful documentation.

Git Annex

There were a few pdfs that I wanted to track with in this repository, but partially because some were still embargoed and because committing binary files to git has issues I decided to use git-annex to track them.

Homepage: git-annex

git-annex is available in Debian, Ubuntu, and OS X Homebrew.

to download the pdfs you would do:

git clone https://github.com/detrout/encode3-curation.git
cd encode3-curiation
git annex init
git annex get <pdf name>

Name		Name	Last commit message	Last commit date
Latest commit History 339 Commits
compare-mad		compare-mad
single_cell_qc		single_cell_qc
.gitignore		.gitignore
CompareTripleLoading.ipynb		CompareTripleLoading.ipynb
Create brians mouse biosamples.ipynb		Create brians mouse biosamples.ipynb
Directional-RNA-Seq-Experienced-User-Card.pdf		Directional-RNA-Seq-Experienced-User-Card.pdf
ENCODESparql.ipynb		ENCODESparql.ipynb
ENCODE_miRNA_experiments_02042016.xlsx		ENCODE_miRNA_experiments_02042016.xlsx
ERCC 1000X sequences for Diane June25_2015.pdf		ERCC 1000X sequences for Diane June25_2015.pdf
Encode2TranscriptsSpikedIn.pdf		Encode2TranscriptsSpikedIn.pdf
Encode3 Pipeline Comparison.ipynb		Encode3 Pipeline Comparison.ipynb
FastqComparisons.ipynb		FastqComparisons.ipynb
Laser capture dissection procedure general protocol_Wold_group.pdf		Laser capture dissection procedure general protocol_Wold_group.pdf
Lookup forced replicate IDs.ipynb		Lookup forced replicate IDs.ipynb
Mouse_e10.5_e12.5.xlsx		Mouse_e10.5_e12.5.xlsx
Plot spike-ins.ipynb		Plot spike-ins.ipynb
QueryPerformance.ipynb		QueryPerformance.ipynb
README.md		README.md
Revised Jackson_quote_August42011.pdf		Revised Jackson_quote_August42011.pdf
SESCC_ENCODE_differentiation_SOPs_May30_2014.pdf		SESCC_ENCODE_differentiation_SOPs_May30_2014.pdf
Status report Sept 27 2011.pdf		Status report Sept 27 2011.pdf
Supplemental_Material.pdf		Supplemental_Material.pdf
Update SESCC protocol.ipynb		Update SESCC protocol.ipynb
Wold_Lab_ATAC_Seq_protocol_December_2016.pdf		Wold_Lab_ATAC_Seq_protocol_December_2016.pdf
biological replicates share biosamples.ipynb		biological replicates share biosamples.ipynb
check fastqs for paired vs single ended sequencing.ipynb		check fastqs for paired vs single ended sequencing.ipynb
check-bokeh-is-working.ipynb		check-bokeh-is-working.ipynb
check-cell-quantity.ipynb		check-cell-quantity.ipynb
check_datawarehouse.py		check_datawarehouse.py
compare biosample mismatches for 822EWO,805QYO,388ZNJ.ipynb		compare biosample mismatches for 822EWO,805QYO,388ZNJ.ipynb
compare encode date_created to library creation date.ipynb		compare encode date_created to library creation date.ipynb
compare-15015-15016-rsem-runs.ipynb		compare-15015-15016-rsem-runs.ipynb
compare_madqc_plots.py		compare_madqc_plots.py
count-atac-reads.ipynb		count-atac-reads.ipynb
curation with ipython notebook.ipynb		curation with ipython notebook.ipynb
curation_common.py		curation_common.py
dcc.fastqs.txt		dcc.fastqs.txt
directional-rna-seq-addendum.pdf		directional-rna-seq-addendum.pdf
download dcc metadata.ipynb		download dcc metadata.ipynb
download-encodedcc.ipynb		download-encodedcc.ipynb
download-ross-rnaseq.ipynb		download-ross-rnaseq.ipynb
e11.5-submission.ipynb		e11.5-submission.ipynb
encode rnaseq evaluation.ipynb		encode rnaseq evaluation.ipynb
encode-201605-upload.ipynb		encode-201605-upload.ipynb
encode-20160729-submission.ipynb		encode-20160729-submission.ipynb
encode-fix-201604.ipynb		encode-fix-201604.ipynb
encode-rabi-lhcn.ipynb		encode-rabi-lhcn.ipynb
encode-rabi-mirna-201602.ipynb		encode-rabi-mirna-201602.ipynb
encode-rabi-mirna-e10.5-e12.5-submission.ipynb		encode-rabi-mirna-e10.5-e12.5-submission.ipynb
encode-rabi-y3q4-submission.ipynb		encode-rabi-y3q4-submission.ipynb
encode-rabi-y4q5-submission.ipynb		encode-rabi-y4q5-submission.ipynb
encode-y2q3-multi-flowcell.ipynb		encode-y2q3-multi-flowcell.ipynb
encode-y2q3-submission.ipynb		encode-y2q3-submission.ipynb
encode-y3q1-e14.5-submission.ipynb		encode-y3q1-e14.5-submission.ipynb
encode-y3q1-in-progress.ipynb		encode-y3q1-in-progress.ipynb
encode-y3q1-submission.ipynb		encode-y3q1-submission.ipynb
encode-y3q2-submission.ipynb		encode-y3q2-submission.ipynb
encode-y3q3 validation.ipynb		encode-y3q3 validation.ipynb
encode-y3q3-submission.ipynb		encode-y3q3-submission.ipynb
encode-y4q1-submission.ipynb		encode-y4q1-submission.ipynb
encode-y4q5-submission.ipynb		encode-y4q5-submission.ipynb
encode2 huvec biosample questions.ipynb		encode2 huvec biosample questions.ipynb
encode2spikes.fa.gz		encode2spikes.fa.gz
encode3-20130920.ttl		encode3-20130920.ttl
encode3-register-proposed-experiments-20140922.ipynb		encode3-register-proposed-experiments-20140922.ipynb
encode3-start.ttl		encode3-start.ttl
encode3-transfection-bar-plot.ipynb		encode3-transfection-bar-plot.ipynb
encode3-y3q3-metadata-cleanup.ipynb		encode3-y3q3-metadata-cleanup.ipynb
experiments.json		experiments.json
experiments.turtle		experiments.turtle
file-extensions.ttl		file-extensions.ttl
find jun 2015 encode submission names.ipynb		find jun 2015 encode submission names.ipynb
find library ids for non-compliant encode experiments.ipynb		find library ids for non-compliant encode experiments.ipynb
find submitted single cell library and flowcell.ipynb		find submitted single cell library and flowcell.ipynb
find-encode2-library-ids.ipynb		find-encode2-library-ids.ipynb
find-experiments-by-biosample.ipynb		find-experiments-by-biosample.ipynb
find-mouse-embryo-tracks.ipynb		find-mouse-embryo-tracks.ipynb
find-mouse-tracks-for-brian.ipynb		find-mouse-tracks-for-brian.ipynb
fix platform and read length for y3q1.ipynb		fix platform and read length for y3q1.ipynb
fix read lengths that were in submitted file name.ipynb		fix read lengths that were in submitted file name.ipynb
fix-h1-hesc-ENCSR643QIZ.ipynb		fix-h1-hesc-ENCSR643QIZ.ipynb
format ENCODE3 Woldlab transfection data.ipynb		format ENCODE3 Woldlab transfection data.ipynb
gencode.v19.annotation.gtf.gz		gencode.v19.annotation.gtf.gz
gencode.vM4.annotation.gtf.gz		gencode.vM4.annotation.gtf.gz
gene-detection-histogram.ipynb		gene-detection-histogram.ipynb
generate-rsem-list-for-ken.ipynb		generate-rsem-list-for-ken.ipynb
georgi.20130825.fastq.txt		georgi.20130825.fastq.txt
georgi.20130920.fastq.txt		georgi.20130920.fastq.txt
georgi.20130925.fastq.txt		georgi.20130925.fastq.txt
georgi.fastqs.txt		georgi.fastqs.txt
georgi.initial.fastq.txt		georgi.initial.fastq.txt
gff2table.py		gff2table.py
group.py		group.py
how-similar-are-indexes-on-HJVYFBCXX.ipynb		how-similar-are-indexes-on-HJVYFBCXX.ipynb
investigate-gtex-biosamples.ipynb		investigate-gtex-biosamples.ipynb
kens-ids.txt		kens-ids.txt
lanes by group.ipynb		lanes by group.ipynb
libraries by starting amount.ipynb		libraries by starting amount.ipynb
librariesWithFlowCellsInReplicates.txt		librariesWithFlowCellsInReplicates.txt
listNeedingPlatformReadLength.tsv		listNeedingPlatformReadLength.tsv

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