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Analysis of the batch retest

Example command line:

In [1]: run crop_reads.py ../sequencing/BatchRetestSample.fastq ../cropped/BatchRetestSample.fa 16

Example command line:

In [2]: run align_batch_retest.py ../cropped/BatchRetestSample.fa BatchRetestSample

The script generates a table of the frequencies with which each individual shRNA was detected in the sequencing data. In the above example, this file will be named BatchRetestSample.counts, located in the subdirectory counts. Once this counts file was successfully generated, files in the directory cropped can be removed.


Example command line:

In [4]: run batch_retest_shRNA_taus.py ../results/Example_BatchRetest ../counts/Example_BatchRetest_t0.counts ../counts/Example_BatchRetest_treated.counts ../growth/Example_BatchRetest_GK.txt

This program creates the output file Prefix.taus, in the same format as the taus file generated by analyze_primary_screen.py, as well as several graphs corresponding to those generated by analyze_primary_screen.py.


Example command line:

In [5]: run batch_retest_shRNA_rhos.py ../results/Example_BatchRetest ../counts/Example_BatchRetest_untreated.counts ../counts/Example_BatchRetest_treated.counts ../growth/Example_BatchRetest_GK.txt

This program creates the output file Prefix.rhos, in the same format as the rhos file generated by analyze_primary_screen.py, as well as several graphs corresponding to those generated by analyze_primary_screen.py.