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Old 05-06-2014, 11:44 PM   #1
trotos
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Location: Cologne,Germany

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Posts: 12
Default ngsplot errors and questions

I tried to find any similar questions but I couldn't

So, I'm under ubuntu 14.04 64bit 32GB memmory

First
is the installation of ngsplot, I followed the guide as it is described (https://code.google.com/p/ngsplot/) for the installation.
2. Add ngsplot executables to your PATH. Under bash, add line like this:

export PATH=~/software/ngsplot/bin:$PATH

to your ~/.bash_profile

3. Set environment variable NGSPLOT like this in your ~/.bash_profile:

export NGSPLOT=~/software/ngsplot

Then in the terminal, execute:

. ~/.bash_profile


as I found out, there is no .bash_profile in my system
second, if I open a new terminal window the system forgets all the paths... the same happens when I restart the system.

so I have to repeat the PATH commands each time.

Is there anythin I can do to make things a little bit more persistent?


Second
I'm using the following command line, but I got an error of unrecognized option

ngs.plot.r -G hg18 -R enhancer -C ~/ngsplot/test.txt -O plottest.enchancer

and I got the following error:

Quote:
Loading R libraries.....Done
Configuring variables...Error in setupVars(args.tbl, default.tbl) :
Unknown region specified. Must be one of: cgi exon genebody tss tes bed
Execution halted
third


And finally...what is with the following message?

In headerIndexBam(bam.list) :
Aligner for: /media/trotos/4TB/WORK/archive/a_60min.sorted.bam cannot be determined. Will automatically convert mapping scores of 255.

\third
Quote:
ngs.plot.r -G hg18 -R bed -E '/media/trotos/4TB/WORK/UCSC/hg18/wgEncodeBroadHmmHuvecHMM.bed' -C ~/ngsplot/SMAD7.txt -O plotSMADstest.Hmmm
Loading R libraries.....Done
Configuring variables...Error in file(file, "rt") : cannot open the connection
Calls: SetupPlotCoord -> ReadBedCoord -> read.table -> file
In addition: Warning messages:
1: In ReadBedCoord(ur) : File name: '-1' does not seem to a correct name
for bed file.

2: In file(file, "rt") : cannot open file '-1': No such file or directory
Execution halted
trotos@UbuStupid:~$ ngs.plot.r -G hg18 -R bed -E '/media/trotos/4TB/WORK/UCSC/hg18/wgEncodeBroadHmmHuvecHMM.bed' -C ~/ngsplot/SMAD.txt -O plotSMADstest.Hmmm
Loading R libraries.....Done
Configuring variables...Error in file(file, "rt") : cannot open the connection
Calls: SetupPlotCoord -> ReadBedCoord -> read.table -> file
In addition: Warning messages:
1: In ReadBedCoord(ur) : File name: '-1' does not seem to a correct name
for bed file.

2: In file(file, "rt") : cannot open file '-1': No such file or directory
Execution halted
the file is

Quote:
/media/trotos/4TB/WORK/archive/a0min.sorted.bam -1 "a0min"
/media/trotos/4TB/WORK/archive/a30min.sorted.bam.bam -1 "a30min"
/media/trotos/4TB/WORK/archive/a60min.sorted.bam.bam -1 "a60min"
/media/trotos/4TB/WORK/archive/b0min_BWA-mem.sorted.bam -1 "b0min"
/media/trotos/4TB/WORK/archive/b30min.sorted.bam.bam -1 "b30min"
/media/trotos/4TB/WORK/archive/b60min.sorted.bam.bam -1 "b60min"
/media/trotos/4TB/WORK/archive/c0min.sorted..bam -1 "c0min"
/media/trotos/4TB/WORK/archive/c30min.sorted..bam -1 "c30min"
/media/trotos/4TB/WORK/archive/c60min.sorted..bam -1 "c60min"
/media/trotos/4TB/WORK/archive/d0min.sorted..bam -1 "d0min"
/media/trotos/4TB/WORK/archive/d30min.sorted..bam -1 "d30min"
/media/trotos/4TB/WORK/archive/d0min.sorted.bam -1 "d60min"
Thank you for your time

Last edited by trotos; 05-07-2014 at 12:20 AM.
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Old 05-07-2014, 12:14 AM   #2
WhatsOEver
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Location: Germany

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Posts: 215
Default

Hi Trotos,

I can only help you with your first problem, as I'm not familiar with ngs.

Depending on your distribution the .bash_profile may be called .profile only. Try to look in your home for such a file using "ls -an".

If you use the export line in the terminal it is only available in that specific terminal, this is normal. When you use a variable in one terminal, it will also not be visible in other ones.

When you have found your .profile file, add the following to the end of your file

export PATH=$PATH:~/software/ngsplot/bin
export NGSPLOT=$NGSPLOT:~/software/ngsplot

(although I think it would also work without the "export")

You will have to log out, log in again to make it working.
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Old 05-13-2014, 05:50 PM   #3
ishmael
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Location: NY, US

Join Date: Jul 2008
Posts: 17
Default

Hi trotos,

I am one of the authors of ngs.plot.
For the second problem, ngs.plot doesn't support enhancer annotation of hg18. You may use hg19.
For the third problem, the format of the configuration should be like this:
/media/trotos/4TB/WORK/archive/a0min.sorted.bam /media/trotos/4TB/WORK/UCSC/hg18/wgEncodeBroadHmmHuvecHMM.bed "a0min"

So in this way ngs.plot could be configured in a more flexible way.

PS, if you have questions about ngs.plot, you are welcome to raise the questions in our google discussion forum. It is:
http://groups.google.com/group/ngsplot-discuss
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Old 05-19-2014, 07:33 AM   #4
trotos
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Location: Cologne,Germany

Join Date: May 2012
Posts: 12
Default

Quote:
Originally Posted by WhatsOEver View Post
Hi Trotos,

I can only help you with your first problem, as I'm not familiar with ngs.

Depending on your distribution the .bash_profile may be called .profile only. Try to look in your home for such a file using "ls -an".

If you use the export line in the terminal it is only available in that specific terminal, this is normal. When you use a variable in one terminal, it will also not be visible in other ones.

When you have found your .profile file, add the following to the end of your file

export PATH=$PATH:~/software/ngsplot/bin
export NGSPLOT=$NGSPLOT:~/software/ngsplot

(although I think it would also work without the "export")

You will have to log out, log in again to make it working.
I fixed this one, I needed to enter something like the following to the very end of ~/.bashrc and only there. anything else didn't work or the system failed to login.


Quote:
export PATH=/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/sbin:/usr/bin:/bin
#export PATH=/media/trotos/documents/NGS_programms/skewer:$PATH
export PATH=~/ngsplot/bin:$PATH
export NGSPLOT=~/ngsplot
export PATH=/media/trotos/documents/NGS_programms/bwa-0.7.8/:$PATH
export PATH=/media/trotos/documents/NGS_programms/bedtools2-2.19.1/bin:$PATH
export PATH=/media/trotos/documents/NGS_programms/MACS2-2.0.10.20131216/bin:$PATH
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Old 05-19-2014, 07:35 AM   #5
trotos
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Location: Cologne,Germany

Join Date: May 2012
Posts: 12
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Quote:
Originally Posted by ishmael View Post
Hi trotos,

I am one of the authors of ngs.plot.
For the second problem, ngs.plot doesn't support enhancer annotation of hg18. You may use hg19.
For the third problem, the format of the configuration should be like this:
/media/trotos/4TB/WORK/archive/a0min.sorted.bam /media/trotos/4TB/WORK/UCSC/hg18/wgEncodeBroadHmmHuvecHMM.bed "a0min"

So in this way ngs.plot could be configured in a more flexible way.

PS, if you have questions about ngs.plot, you are welcome to raise the questions in our google discussion forum. It is:
http://groups.google.com/group/ngsplot-discuss
Is there any way to annotate the enchancers???
I will really need this answer.
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Old 05-20-2014, 06:54 AM   #6
ishmael
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Location: NY, US

Join Date: Jul 2008
Posts: 17
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Quote:
Originally Posted by trotos View Post
Is there any way to annotate the enchancers???
I will really need this answer.
If you want enhancers on hg18, you may need to generate an enhancer annotation in bed format yourself.
Download the enhancer annotation from encode project, and then use liftover of UCSC to convert the coordinations from hg19 to hg18, and then feed this bed to ngsplot, it should work.
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