Scripture output

[wenhuang]

Hi,

Does anybody know what is the fifth column in a Scriputure (http://www.broadinstitute.org/software/scripture/) bed output for?

The documentation says Scripture also outputs RPKM, and this is the only column that appears to be RPKM, but why all single exon transcripts have zero value (see attached example)?

chr29   194202  195851  chr29:194202-195851     0.0     *       194202  195851  0,0,0   1       1649,   0,
chr29   376781  377122  chr29:376781-377122     0.0     *       376781  377122  0,0,0   1       341,    0,
chr29   587298  607378  chr29:587298-607378     94.0    -       587298  607378  0,0,0   6       1377,160,118,138,185,35,        0,2848,465
3,7626,18776,20045,
chr29   587298  607378  chr29:587298-607378     68.0    -       587298  607378  0,0,0   6       1377,142,118,138,185,35,        0,2866,465
3,7626,18776,20045,
chr29   587298  607378  chr29:587298-607378     15.0    -       587298  607378  0,0,0   4       1377,138,185,35,        0,7626,18776,20045
,

Thank you very much!

[jinjun]

You may want to use 'score' task (-task score option) to get the full output including conf values.