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2016-12-13
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* Organize files by organism -> cell_type -> tf/hm -> (biorep1, biorep2, idr)
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2017-01-13
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* Modify ExpressOrtho perl script to confirm to perl style standards.
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* Fetch bams or fastqs.
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* Specify file accession for control and experiment instead of experiment accession.
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* Add IDR for 2 replicates. Wait on response to figure out. (IDR / FDR?)
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* MongoDB read only database to clone. MongoDB helper scripts to update database. Need to create own db instance for saving results.
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* Don't need to save output files back to the database.
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* Generate report log at the end.
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* Remove Duplicates yes / no & duplicates.
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* Pooled & Pseudo replicates - pooled concatenate, pseudo shuffled (bam -> sam for plaintext). Configurable option.
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* Sphinx documentation at the same time. |
