downloading the CD4 methylCRF dataset

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edm...@gmail.com

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Sep 5, 2014, 4:48:29 PM9/5/14

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Hello,

I'm interested in inspecting the methylCRF results for T-cells (e.g. Database: hg19 Primary Table: TC007CD4N_mCRF). I could find it on the Table Browser http://genomebrowser.wustl.edu/cgi-bin/hgTables but can not download more than 10M lines per table.

Is there a ftp server for download? /srv/epg/data/hg19/methylCRF/TC007CD4N_mCRF.bwg

edm...@gmail.com

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Sep 7, 2014, 1:11:43 PM9/7/14

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Hello,

I tried to run the example dataset as described but ran into error. Below is the "err". I checked that the directory is in my path but after sourcing ~/.bashrc, the command "olapBed" is not recognized. What else should I check? Thank you, -Ed

$ more err

Sun Sep 7 11:48:17 2014 format H1ESmrg_DIP.bed and H1ESmrg_MRE.bed

/stornext/snfs5/cancer-analysis/users/ec1/app/methylcrf/medip_norm.sh: line 34: olapBed: command not found

-rw-r--r-- 1 ec1 can 0 Sep 7 11:48 cpg_H1ESmrg_DIP_read.bed

expr: non-numeric argument

p75: P75cnt:

/stornext/snfs5/cancer-analysis/users/ec1/app/methylcrf/medip_norm.sh: line 44: olapBed: command not found

-rw-r--r-- 1 ec1 can 1674966247 Dec 27 2012 H1ESmrg_DIP.bed

-rw-r--r-- 1 ec1 can 0 Sep 7 11:48 H1ESmrg_DIP.bed.norm.bed

-rw-r--r-- 1 ec1 can 59456634 Dec 27 2012 H1ESmrg_MRE.bed

Sun Sep 7 11:48:17 2014 make avg windows for H1ESmrg_DIP.bed and H1ESmrg_MRE.bed

/stornext/snfs5/cancer-analysis/users/ec1/app/methylcrf/bed2avgwinbin.sh: line 34: olapBed: command not found

100

/stornext/snfs5/cancer-analysis/users/ec1/app/methylcrf/bed2avgwinbin.sh: line 34: olapBed: command not found

1000

/stornext/snfs5/cancer-analysis/users/ec1/app/methylcrf/bed2avgwinbin.sh: line 34: olapBed: command not found

10000

/stornext/snfs5/cancer-analysis/users/ec1/app/methylcrf/bed2avgwinbin.sh: line 34: olapBed: command not found

100

/stornext/snfs5/cancer-analysis/users/ec1/app/methylcrf/bed2avgwinbin.sh: line 34: olapBed: command not found

1000

/stornext/snfs5/cancer-analysis/users/ec1/app/methylcrf/bed2avgwinbin.sh: line 34: olapBed: command not found

10000

/stornext/snfs5/cancer-analysis/users/ec1/app/methylcrf/bed2avgwinbin.sh: line 34: olapBed: command not found

0 0 0 H1ES_DIP_d0.cnt

0 0 0 H1ES_MRE_d0.cnt

0 0 0 H1ES_DIP_d10.cnt

0 0 0 H1ES_MRE_d10.cnt

0 0 0 H1ES_DIP_d100.cnt

0 0 0 H1ES_MRE_d100.cnt

0 0 0 H1ES_DIP_d1000.cnt

0 0 0 H1ES_MRE_d1000.cnt

0 0 0 H1ES_DIP_d10000.cnt

0 0 0 H1ES_MRE_d10000.cnt

H1ES_DIPMRE.cnt column numbers

Sun Sep 7 11:59:58 2014 making DIPMRE.cnt for H1ESmrg_DIP.bed and H1ESmrg_MRE.bed

H1ES_DIPMRE.cnt column numbers

Sun Sep 7 11:59:59 2014 make table

readline failed: [IO::File::AutoChomp=GLOB(0x1c3ba88)] () at ./methylCRF.pl line 33.

michael

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Sep 7, 2014, 2:30:53 PM9/7/14

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Hi Ed,

hmm, interesting, two questions. Is the current directory in your path,
ie .? Also, did olapBed successfully build, ie, is the executable there?

best,
michael

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Edmund Chang

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Sep 8, 2014, 3:25:28 PM9/8/14

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Hi Michael,

I tried to compile methylcrf on my mac after using git to download the program. I encountered an error when running "make". Attached is the error message. -Ed

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methylcrf_make_error.txt

edm...@gmail.com

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Sep 10, 2014, 8:07:20 PM9/10/14

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Has anyone encountered a problem with compiling methylcrf on their computer?

On Friday, September 5, 2014 3:48:29 PM UTC-5, edm...@gmail.com wrote:

michael

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Sep 10, 2014, 11:18:51 PM9/10/14

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Hi Edmond,

It looks like OSX doesn't have argp.h which is a glibc thing. You can
google for instructions on how to install it, but it looks a little
involved.

I'm planning to take out this dependency, but I just don't have time at
the moment -sorry. I'll try to get to it soon.

In the meantime, do you have a linux server you can run methylCRF on?

best,
michael

On 09/08/14 14:24, Edmund Chang wrote:
> Hi Michael,
>
> I tried to compile methylcrf on my mac after using git to download the
> program. I encountered an error when running "make". Attached is the
> error message. -Ed
>
> On Sun, Sep 7, 2014 at 1:30 PM, michael <ste...@seas.wustl.edu
> <mailto:ste...@seas.wustl.edu>> wrote:
>
> Hi Ed,
>
> hmm, interesting, two questions. Is the current directory in your
> path, ie .? Also, did olapBed successfully build, ie, is the
> executable there?
>
> best,
> michael
>
>
>
> On 09/07/14 12:11, edm...@gmail.com <mailto:edm...@gmail.com> wrote:
>
> Hello,
> I tried to run the example dataset as described but ran into error.
> Below is the "err". I checked that the directory is in my
> path but
> after sourcing ~/.bashrc, the command "olapBed" is not
> recognized. What
> else should I check? Thank you, -Ed
>
> $ more err
> Sun Sep 7 11:48:17 2014 format H1ESmrg_DIP.bed and H1ESmrg_MRE.bed

> /stornext/snfs5/cancer-__analysis/users/ec1/app/__methylcrf/medip_norm.sh:

> line 34: olapBed: command not found
> -rw-r--r-- 1 ec1 can 0 Sep 7 11:48 cpg_H1ESmrg_DIP_read.bed
> expr: non-numeric argument
> p75: P75cnt:

> /stornext/snfs5/cancer-__analysis/users/ec1/app/__methylcrf/medip_norm.sh:

> line 44: olapBed: command not found
> -rw-r--r-- 1 ec1 can 1674966247 Dec 27 2012 H1ESmrg_DIP.bed
> -rw-r--r-- 1 ec1 can 0 Sep 7 11:48
> H1ESmrg_DIP.bed.norm.bed
> -rw-r--r-- 1 ec1 can 59456634 Dec 27 2012 H1ESmrg_MRE.bed
> Sun Sep 7 11:48:17 2014 make avg windows for H1ESmrg_DIP.bed and
> H1ESmrg_MRE.bed
> 0