function "loadGTF" is losing

[weiwsmiling]

Dear Zhang,

I am trying to analysis the PARIS data as you introduced in the Nature paper. However, when using samPairingCalling.pl, "Memory/Usage.pm" can not be found. So I use samPairingCalling.new.pl and find this one can work. It use the function "loadGTF" to read gtf file, right? But it is fail to find the "loadGTF" function in module "PARISutil" actually. And I read the PARISutil code, it does not has the function as well. What's the problem ?

Thanks!
Wei

[qczhang]

Hi Wei, thank you for your interest and your question. Usage.pm is only for debug purpose to find out how much memory you need to run your program. You can install the module (from CPAN) on your own if you want to enable this functionality.

I know this might be a little confusing, but samPairingCalling.test.pl is the one really the final version. The loadGTF function is not used in this program as you can see - just run it without providing an annotation file and it will go through. The annotation and annotation-based filtering are actually done in annotateTrans.test.pl script.

Thanks,
Cliff

On Jun 1, 2016, at 5:31 PM, wu wei <notifications@github.commailto:notifications@github.com> wrote:

Dear Zhang,

I am trying to analysis the PARIS data as you introduced in the Nature paper. However, when using samPairingCalling.pl, "Memory/Usage.pm" can not be found. So I use samPairingCalling.new.pl and find this one can work. It use the function "loadGTF" to read gtf file, right? But it is fail to find the "loadGTF" function in module "PARISutil" actually. And I read the PARISutil code, it does not has the function as well. What's the problem ?

Thanks!
Wei

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[weiwsmiling]

It works! Thanks a lot for your generous help!

Best,
Wei

[Janderscan]

Dear Zhang,

I was also trying to understand your script and missed the loadGTF; then I saw this post. I have a small question related to this: without using the annotation, maxND returns just the largest gap in the read and omit other gaps. Then, if there are two gaps in the read and the largest is just a intron, the other gap (potentially informative) will not be considered in the analysis. I guess it is not unusual that one strand of the crosslinked dsRNA overlaps a junction and therefore the informative gap in the read is the shorter one. Am I missing something?

Thanks for your time.