|
|
|
2016-02-25
|
|
|
|
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.
|
|
|
|
|
|
|
|
* 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.
|
|
|
|
|
|
|
|
2016-03-03
|
|
|
|
============
|
|
|
|
|
|
|
|
* Run on Myc / Max -- wait on correct experiments to use!
|
|
|
|
* Nothing else!
|
|
|
|
|
|
|
|
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
|
|
|
|
|
|
|
|
2016-03-17
|
|
|
|
============
|
|
|
|
|
|
|
|
* 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)!?
|
|
|
|
|
|
|
|
2016-04-05
|
|
|
|
2016-12-13
|
|
|
|
============
|
|
|
|
* Created dummy sample entries to run pipeline faster!
|
|
|
|
* Look into better downloading tools to increase speed
|
|
|
|
* Organize files by organism -> cell_type -> tf/hm -> (biorep1, biorep2, idr)
|
|
|
|
|
|
|
|
2016-04-12
|
|
|
|
2016-12-07
|
|
|
|
=============
|
|
|
|
* Add gem
|
|
|
|
* For DFBS: macs2, csaw, jmosaic
|
|
|
|
* 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
|
|
|
|
=============
|
| ... | ... | @@ -53,28 +36,47 @@ End Goals: |
|
|
|
* Merged replicates in workflow
|
|
|
|
* Don't need GUI
|
|
|
|
|
|
|
|
2016-09-22
|
|
|
|
===============
|
|
|
|
* macs2 paired end reads need to be run differently check accordingly.
|
|
|
|
* convert/sort/idr for individual samples.
|
|
|
|
|
|
|
|
2016-12-07
|
|
|
|
2016-04-12
|
|
|
|
=============
|
|
|
|
* Human: CHD2 for k562 H1-hESC cells
|
|
|
|
* Add gem
|
|
|
|
* For DFBS: macs2, csaw, jmosaic
|
|
|
|
|
|
|
|
2016-12-13
|
|
|
|
2016-04-05
|
|
|
|
============
|
|
|
|
* Organize files by organism -> cell_type -> tf/hm -> (biorep1, biorep2, idr)
|
|
|
|
* Created dummy sample entries to run pipeline faster!
|
|
|
|
* Look into better downloading tools to increase speed
|
|
|
|
|
|
|
|
2017-01-13
|
|
|
|
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
|
|
|
|
===========
|
|
|
|
* 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. |
|
|
|
|
|
|
|
* 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.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
