ReadDepth manual or example

papori · 07-09-2015, 06:28 AM

Hi all,
Do u know where can i find the manual or normal example of ReadDepth tool?
not the same example as here:
https://github.com/chrisamiller/readdepth
Its not detailed enough...
it R package, but i cant find it..
Thanks,
Pap

papori · 07-13-2015, 04:51 AM

Any ideas for how to use this package?
Thanks,
Pap

GenoMax · 07-13-2015, 05:07 AM

Have you looked at the text here: https://github.com/chrisamiller/read...n/readDepth.Rd

If that is not detailed enough you should email the author directly for additional help: https://github.com/chrisamiller

papori · 07-13-2015, 05:15 AM

Quote:

Originally Posted by GenoMax

Have you looked at the text here: https://github.com/chrisamiller/read...n/readDepth.Rd

If that is not detailed enough you should email the author directly for additional help: https://github.com/chrisamiller

Hi GenoMax,
Yes, i saw this already and it's not detailed enough, at least for me..
I sent email to the author and waiting for his response..
I was sure that every package in R must have vignette/ or at least simple manual..

Thanks,
Pap

papori · 07-14-2015, 02:59 AM

Ok, he didnt answer me yet..
In the meanwhile, can u reccomened on a easy to execute tool for exploring the read depth over the human genome?
Thanks,
Pap

GenoMax · 07-14-2015, 08:35 AM

How about genomecov (http://bedtools.readthedocs.org/en/l...genomecov.html) or coveragebed (http://bedtools.readthedocs.org/en/l...overage.html)? Those should work for what you are trying to do.

papori · 07-15-2015, 02:07 PM

Quote:

Originally Posted by GenoMax

How about genomecov (http://bedtools.readthedocs.org/en/l...genomecov.html) or coveragebed (http://bedtools.readthedocs.org/en/l...overage.html)? Those should work for what you are trying to do.

ohh cool!
Thanks!! I like bedtools!

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07-09-2015, 06:28 AM	#1
papori Senior Member Location: berd Join Date: Dec 2010 Posts: 181	ReadDepth manual or example Hi all, Do u know where can i find the manual or normal example of ReadDepth tool? not the same example as here: https://github.com/chrisamiller/readdepth Its not detailed enough... it R package, but i cant find it.. Thanks, Pap

07-13-2015, 04:51 AM	#2
papori Senior Member Location: berd Join Date: Dec 2010 Posts: 181	Any ideas for how to use this package? Thanks, Pap

07-13-2015, 05:07 AM	#3
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	Have you looked at the text here: https://github.com/chrisamiller/read...n/readDepth.Rd If that is not detailed enough you should email the author directly for additional help: https://github.com/chrisamiller

07-14-2015, 02:59 AM	#5
papori Senior Member Location: berd Join Date: Dec 2010 Posts: 181	Ok, he didnt answer me yet.. In the meanwhile, can u reccomened on a easy to execute tool for exploring the read depth over the human genome? Thanks, Pap

07-14-2015, 08:35 AM	#6
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	How about genomecov (http://bedtools.readthedocs.org/en/l...genomecov.html) or coveragebed (http://bedtools.readthedocs.org/en/l...overage.html)? Those should work for what you are trying to do.