Mercurial > repos > galaxy-australia > smudgeplot

annotate test-data/my_genome_warnings.txt @ 3:24e471d13fe9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
author iuc
date Thu, 30 Jun 2022 22:45:21 +0000
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24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
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24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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2 ######################
24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
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3 ## INPUT PROCESSING ##
24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
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4 ######################
24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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6 #############
24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
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7 ## SUMMARY ##
24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
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8 #############
24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
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9 detecting two smudges at the same positions, not enough data for this number of bins lowering number of bins to 35
24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
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10 detecting two smudges at the same positions, not enough data for this number of bins lowering number of bins to 30
24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
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11 detecting two smudges at the same positions, not enough data for this number of bins lowering number of bins to 25
24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
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12 detecting two smudges at the same positions, not enough data for this number of bins lowering number of bins to 20
24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
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13 !! Warning, your coverage filter on the lower end (L = 23 ) is higher than half of the 1n coverage estimate ( 1n / 2 = 12.5
24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
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14 If the real 1n coverage is half of your estimate you would not picked it up due to the filtering.
24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
iuc
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15 If you have sufficient coverage, consider reruning the analysis with lower L (something like (1n / 2) - 5)
24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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16 One good way for verificaiton would be to compare it to GenomeScope estimate of haploid coverage
24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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18 ##########
24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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19 ## PLOT ##
24e471d13fe9 planemo upload for repository https://github.com/galaxyproject/tools-iuc commit cbe90253166d9908b68beb36b9488478178d225b
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20 ##########