SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   Scripture output (http://seqanswers.com/forums/showthread.php?t=5796)

wenhuang 07-01-2010 11:00 AM

Scripture output
 
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)?

Code:

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 07-28-2010 03:36 AM

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


All times are GMT -8. The time now is 03:42 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.