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knights-lab / analysis_SHOGUN

Analysis scripts and code for reproducing the analysis for the SHOGUN paper
MIT License
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Clinical dataset validation #8

Open bhillmann opened 7 years ago

bhillmann commented 7 years ago

@RRShieldsCutler Has some of these datasets

bhillmann commented 7 years ago

@RRShieldsCutler I added the folder below with the README for this task:

clinical_datasets/

How close is the final dataset to running?

I would like to use strandex to subsample these FASTQs after quality control and run them all with SHOGUN RefSeq and IMG.

RRShieldsCutler commented 7 years ago

Sorry just saw this (git only emailed me the text "clinical_datasets" and none of your questions).

I ran shizen without flash on the dataset, trim_l to 50. I downsampled the R1's to 500k reads. Also converted both the deep and shallow to fasta. All those files are in this directory: /project/flatiron2/data/public_shotgun/karlsson2013/shizen_20161130

Yesterday I ran shogun on both the deep and shallow set using utree_abfvh. Results are located: Original depth: /project/flatiron2/robin/results/shogun_analysis_karlsson/deep_shotgun Downsample: /project/flatiron2/robin/results/shogun_analysis_karlsson/shallow/

From this dataset http://www.nature.com/nature/journal/v498/n7452/full/nature12198.html

bhillmann commented 7 years ago

Can you rerun the commands with the newest UTree versions?

RRShieldsCutler commented 7 years ago

Yup. Running currently, they should be done by the evening sometime. They'll be in the same directories as pasted above.

RRShieldsCutler commented 7 years ago

Both are finished, FYI. I confirmed that the confidence intervals are updated in the tsv files. Original depth: /project/flatiron2/robin/results/shogun_analysis_karlsson/deep_shotgun Downsample: /project/flatiron2/robin/results/shogun_analysis_karlsson/shallow/

bhillmann commented 7 years ago

Awesome, great work.

bhillmann commented 7 years ago 
/project/flatiron2/data/public_shotgun/karlsson2013/map.txt
RRShieldsCutler commented 7 years ago

Currently re-running with the new complete-species utree. The deep (full reads) should finish tonight sometime here:

/project/flatiron2/robin/results/shogun_analysis_karlsson/161208_analysis/deep/shogun_utree_lca_out

The shallow (downsampled) reanalysis is complete and located here:

/project/flatiron2/robin/results/shogun_analysis_karlsson/161208_analysis/shallow/shogun_utree_lca_out