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CAMBa Tilling Pipeline Run Directions:
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1. Make directory 'TillingN', where N is the current tilling run number.
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2. Copy 'create scripts.py' into that directory.
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3. Make sure that you have the following pipeline input files in the following 
directories and subdirectories:

TillingN:
	List_of_genes_and_homologs_by_organism
	sequence_URL_file

TillingN/Sequence_Files:
	tilling_seqs.txt

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Information on how to structure each
input file is included below:
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i. The format of List_of_genes_and_homologs_by_organism should be:

Organism: <organism_x>
<gene_1>
( <homolog_1a> <homolog_1b> )
...

Organism: <organism_y>
...

where <organism> may be 'Oryza_sativa', 'Triticum_durum', or
'Solanum_lycopersicum.'

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ii. The format for sequence_URL_file should be:

LibraryName
URL of associated 's_N_sequence.txt' file
LibraryName
URL of associated 's_N_sequence.txt' file
...

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iii. 'tilling_seqs.txt' should be a fasta file.

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4. Run ./create_scripts.py <tilling_run_number> <number_of_pooling_dimensions>

For Tilling3 and Tilling5, the TILLING experiments described in the CAMBa paper,
"number_of_pooling_dimensions" is 2, reflecting the two-dimensional pooling
scheme.
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5. create_scripts.py should generate a set of scripts:

	./generated_setup_script.sh
	./generated_run_script.sh
	./generated_run_script_2.sh

copy over several more scripts from 'TILLING/scripts',
and print out instructions on running the pipeline.
Following these instructions will result in the pipeline being run
automatically.

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6. The resulting mutation candidates files will be created without a header.  
The mutation candidates file header is stored in the 'TILLING/misc' directory.
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Please report any problems to me at vmissirian@ucdavis.edu
