The meaning of SCRIPTURE output file, *.segments

Question

[zonghongz]

I am using SCRIPTURE to do transcriptome reconstruction, the final output are *.segments file and *.dot file.

Could anyone explain what does each column mean in the *.segments file?

Here is an example of few lines in this .segments file,

chr7    141237686       141248606       chr7:141237686-141248606        591.0   +       141237686       141248606       0,0,0   6       16,84,119,2014,176,227, 0,3198,6091,7244,9534,10693,

chr7    141237686       141248606       chr7:141237686-141248606        411.0   +       141237686       141248606       0,0,0   6       16,84,119,2014,170,227, 0,3198,6091,7244,9540,10693,

chr7    141237686       141248606       chr7:141237686-141248606        740.0   +       141237686       141248606       0,0,0   6       16,84,119,98,176,227,   0,3198,6091,9160,9534,10693,

chr7    141237686       141248606       chr7:141237686-141248606        560.0   +       141237686       141248606       0,0,0   6       16,84,119,98,170,227,   0,3198,6091,9160,9540,10693,

chr7    141237686       141248606       chr7:141237686-141248606        589.0   +       141237686       141248606       0,0,0   6       16,84,683,2067,176,227, 0,3198,6091,7191,9534,10693,

chr7    141237686       141248606       chr7:141237686-141248606        409.0   +       141237686       141248606       0,0,0   6       16,84,683,2067,170,227, 0,3198,6091,7191,9540,10693,
......

I would appreciate if anyone may help!

Zong

Answer 1

[michael.ante]

Hi Zong,

this looks like a standard bed-file (see documentation). If you have a look at Scripture's manual (here), it tells you that the output next to the dot file is a bed file.

Cheers,

Michael

[zonghongz]

Thank you, Michael,

Yes, it is bed-file, what I would like to know is what these number stands for? especially, what do numbers in column5, column9-11 mean?

thanks

Zong

[zonghongz]

Thanks Michael,

After reading bed-file instruction, I think figure out what these column mean.

cheers

Zong