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meeting notes

Last edited by Adam Caprez

2017-05-02

  • Finish adding the peak calling tools.
  • Start work on the pegasus paper.
  • 3 papers. Dual computational (Pegasus pipeline) / biological papers, resubmit express ortho.

2017-04-13

  • PePR, Hidden Domains, & Music tests are working, need to get them implemented
  • More Documentation! Especially getting read the docs setup.
  • XSede stuff too! Very close.

2017-03-31

  • Zerone
  • PePR
  • Hidden Domains
  • MUSIC
  • Documentation
  • Create skeleton of paper

2017-03-15

  • Need to decide how to handle spp broad peaks.
  • Further work to get MUSIC, PEPR, CHILLIN, ZERONE
  • Download update encode json dump

2017-03-09

  • Download updated encode json dump and update
  • Get broad/narrow peaks & idr in by next week
  • Bridges
  • Cleanup database tables.

2017-02-23

  • Work toward getting bridges up & running by the end of next week.
  • Decide on full research allocation for Bridges.
  • Get new peak calling tools.

2017-02-09

  • No NIH :(
  • Express Ortho paper review & resubmit
  • Mini tool comparison for ~10 tools, talk to developers
  • March 13th / Great Lakes Conference abstract due
  • Dual paper submit, have pegasus ready for submission.

2017-01-26

  • Great Lakes Conference in Chicago May 15-17th
  • Review Paper by Monday, Deadline for submission is next Wednesday
  • Generate new swooshy flow chart for the workflow
  • Think about scoring algorithm for different peak calling tool
  • Add idr granularity
  • Keep using random pairing for control / signal
  • Adjust signal input to list
  • Validate idr specification / narrow & broad peak specification
  • Generate read distribution from bam, otherwise use default
  • Create default ccat config file.
  • Remove peakranger gene annotation file

2017-01-13

  • Modify ExpressOrtho perl script to confirm to perl style standards.
  • Fetch bams or fastqs.
  • Specify file accession for control and experiment instead of experiment accession.
  • Add IDR for 2 replicates. Wait on response to figure out. (IDR / FDR?)
  • MongoDB read only database to clone. MongoDB helper scripts to update database. Need to create own db instance for saving results.
  • Don't need to save output files back to the database.
  • Generate report log at the end.
  • Remove Duplicates yes / no & duplicates.
  • Pooled & Pseudo replicates - pooled concatenate, pseudo shuffled (bam -> sam for plaintext). Configurable option.
  • Sphinx documentation at the same time.

2016-12-13

  • Organize files by organism -> cell_type -> tf/hm -> (biorep1, biorep2, idr)

2016-12-07

  • Human: CHD2 for k562 H1-hESC cells

2016-09-22

  • macs2 paired end reads need to be run differently check accordingly.
  • convert/sort/idr for individual samples.

2016-09-15

  • Grant application in April, hear back in May
  • Mirrored papers, ChIPathlon / Biological.
  • Next steps: Re run human / mouse with individual samples, run idr on the output.
  • CH12.lx / GM12878 if time permits. End Goals:
  • IDR in workflow
  • Pooled/Pseudo replicates in workflow
  • Merged replicates in workflow
  • Don't need GUI

2016-04-12

  • Add gem
  • For DFBS: macs2, csaw, jmosaic

2016-04-05

  • Created dummy sample entries to run pipeline faster!
  • Look into better downloading tools to increase speed

2016-03-17

  • Potentially do comparison paper of no SQL -> sql for bioinformatics. Run similar setup/design/analysis in SQL and see how it compares.
  • 3 Papers (Biological paper, Pegasus paper, MongoDB paper)!?

2016-03-10

  • Don't use the assembly from the samples record, use the Grch assembly.
  • bowtie2 standard error continues quality measures!
  • for now focus on bowtie2
  • MXI1
  • Add aggregation pipelines to meta to extract relevant transcription factors

2016-03-03

  • Run on Myc / Max -- wait on correct experiments to use!
  • Nothing else!

2016-02-25

  • Most conditions don't exist, exist for some.
  • Collapse Bed & Peak Collections
  • Only need one of score or signal_value
  • Need to derive read length from downloaded fastq
  • Randomly select experiment to control for peak calling, only use possible_controls
  • Only need human / mouse
  • DFBS keep everything same except one of condition OR cell type. (ignore for now)
  • Restrict to database, add genome collection.

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