Scripture -windows argument

[apredeus]

To anyone coming across this thread because they can't figure out how to set Scripture's -windows flag (Which is listed as optional in the documentation, but seems mandatory when running scripture.jar):

This problem can also be solved by using the latest beta-2 build, which is available from http://www.broadinstitute.org/softwa...re/?q=download

Thank you, this was very helpful.

[Eric Fournier]

To anyone coming across this thread because they can't figure out how to set Scripture's -windows flag (Which is listed as optional in the documentation, but seems mandatory when running scripture.jar):

This problem can also be solved by using the latest beta-2 build, which is available from http://www.broadinstitute.org/softwa...re/?q=download

[avi]

Hi,

I am new to next-gen sequencing, so this might be a very obvious question. But still..

I am trying to use Scripture for my work. But I am not able to figure out how the -windows argument for scripture needs to be specified. The documentation on the website calls it an optional argument and doesn't give much details about it.. But the version of scripture available for download requires it as mandatory argument.

I want to do transcript calling over the entire Chromosome and not just a window of it. So I was looking to do something like 1- 2992546. But Scripture throws an error for it. I ve also tried alternatives like 1:2992546 or 1,2992546 with no luck. Can someone tell me how I should be doing this?

Also, on a slightly unrelated note what exactly is a maskfile and how can I make one?

thanks