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  • how to understand the output result of PacBio_BasSummary

    Hello there,
    I run PacBio_BasSummary.py program, but I can't understand the result. I want to calculate Productivity 0 (%), Productivity 1 (%), Productivity 2 (%) in command-line. Could someone help to explain ? I'd appreciate that.

    PHP Code:
    longest read was ZMW 159241 at 106496 bases

    statistics 
    for subreads:

     
    reads subreads       bases    avg     max     ZMW  criterion

    163482  2001836  5251467935   2623   94763  159241  Total
    150292  1983394  5207608109   2625   94763  159241  
    --Sequencing
     21870    22683    14034460    618    3839   11438  
    ----Productivity-0
     47816   479854  2021505261   4212   94763  159241  
    ----Productivity-2
     80606  1480857  3172068388   2142   79783  113375  
    ----Productivity-1
     80599  1480776  3171771916   2141   79783  113375  
    ------HQ Len >= 50
     80599  1480776  3171771916   2141   79783  113375  
    --------HQ Score >= 750
     80598  1480706  3171735760   2142   79783  113375  
    ----------Avg Insert >= 100
     80598  1058605  1464546526   1383   56859   73513  
    ----------HQ Bases
         0        0           0      0       0      
    -1  ------------Consensus Reads 

  • #2
    Originally posted by lingling huang View Post
    Hello there,
    I run PacBio_BasSummary.py program, but I can't understand the result. I want to calculate Productivity 0 (%), Productivity 1 (%), Productivity 2 (%) in command-line. Could someone help to explain ? I'd appreciate that.

    PHP Code:
    longest read was ZMW 159241 at 106496 bases

    statistics 
    for subreads:

     
    reads subreads       bases    avg     max     ZMW  criterion

    163482  2001836  5251467935   2623   94763  159241  Total
    150292  1983394  5207608109   2625   94763  159241  
    --Sequencing
     21870    22683    14034460    618    3839   11438  
    ----Productivity-0
     47816   479854  2021505261   4212   94763  159241  
    ----Productivity-2
     80606  1480857  3172068388   2142   79783  113375  
    ----Productivity-1
     80599  1480776  3171771916   2141   79783  113375  
    ------HQ Len >= 50
     80599  1480776  3171771916   2141   79783  113375  
    --------HQ Score >= 750
     80598  1480706  3171735760   2142   79783  113375  
    ----------Avg Insert >= 100
     80598  1058605  1464546526   1383   56859   73513  
    ----------HQ Bases
         0        0           0      0       0      
    -1  ------------Consensus Reads 
    The numbers are in the first column -

    Productivity-0: 21870 / 150292 total = 14.6%
    Productivity-1: 80606 / 150292 total = 53.6%
    Productivity-2: 47816 / 150292 total = 31.8%

    Comment


    • #3
      Originally posted by gconcepcion View Post
      The numbers are in the first column -

      Productivity-0: 21870 / 150292 total = 14.6%
      Productivity-1: 80606 / 150292 total = 53.6%
      Productivity-2: 47816 / 150292 total = 31.8%
      I see. Thanks a lot.

      Comment

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