Re: Not including fragment map?

[Neva Durand]

Look at your other log files. For example for launching the jobs it should tell you what site file. You might have specified a file path that it couldn’t find when it ran. 

What was the command you used to run?

On Thu, Mar 22, 2018 at 7:57 AM shen Eric <swei...@gmail.com> wrote:

Hi,

    I just found that my result hic file doesn't contain fragment resolusioin. and I checked the shell script and log file.

    I did specify a site_file, but why the juicebox_tools pre logfile says "Not including fragment map"?

Thanks

--
You received this message because you are subscribed to the Google Groups "3D Genomics" group.
To unsubscribe from this group and stop receiving emails from it, send an email to 3d-genomics...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/c2a0ae89-0b4b-4fad-b593-2ec5c0dc3f21%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org

[Neva Durand]

Does your restriction site file exist at /path/to/dm3_DpnII.txt  ?

On Fri, Mar 23, 2018 at 10:06 PM, shen Eric <swei...@gmail.com> wrote:

Here is my command :
juicer.sh -g dm3 -s DpnII -p  /path/to/dm3.chrom.sizes -y /path/to/dm3_DpnII.txt -z /path/to/dm3.fa


在 2018年3月22日星期四 UTC+8下午8:27:08，Neva Durand写道：

To unsubscribe from this group and stop receiving emails from it, send an email to 3d-genomics+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/f68f43dc-43b0-4aa3-8615-83e26d6984dd%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

[Neva Durand]

What was your command using Juicer Tools pre?

On Sun, Apr 8, 2018 at 4:22 AM, shen Eric <swei...@gmail.com> wrote:

sorry for the delay, but I checked these path and I'm sure they are correct.

And I tried to use juicerbox_tools.jar pre to generate .hic file, still didn't get fragment resolusion.

在 2018年3月27日星期二 UTC+8下午9:33:56，Neva Durand写道：

Does your restriction site file exist at /path/to/dm3_DpnII.txt  ?

On Fri, Mar 23, 2018 at 10:06 PM, shen Eric <swei...@gmail.com> wrote:

Here is my command :
juicer.sh -g dm3 -s DpnII -p  /path/to/dm3.chrom.sizes -y /path/to/dm3_DpnII.txt -z /path/to/dm3.fa


在 2018年3月22日星期四 UTC+8下午8:27:08，Neva Durand写道：

Look at your other log files. For example for launching the jobs it should tell you what site file. You might have specified a file path that it couldn’t find when it ran. 

What was the command you used to run?

On Thu, Mar 22, 2018 at 7:57 AM shen Eric <swei...@gmail.com> wrote:

Hi,

    I just found that my result hic file doesn't contain fragment resolusioin. and I checked the shell script and log file.

    I did specify a site_file, but why the juicebox_tools pre logfile says "Not including fragment map"?

Thanks

--
You received this message because you are subscribed to the Google Groups "3D Genomics" group.
To unsubscribe from this group and stop receiving emails from it, send an email to 3d-genomics...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/c2a0ae89-0b4b-4fad-b593-2ec5c0dc3f21%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org

--
You received this message because you are subscribed to the Google Groups "3D Genomics" group.
To unsubscribe from this group and stop receiving emails from it, send an email to 3d-genomics...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/f68f43dc-43b0-4aa3-8615-83e26d6984dd%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

--

Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org

--
You received this message because you are subscribed to the Google Groups "3D Genomics" group.
To unsubscribe from this group and stop receiving emails from it, send an email to 3d-genomics+unsubscribe@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/094e3a4b-0ecc-4004-baa6-c898fafe2e57%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

[shen Eric]

I found the reason.
It's because I use an old version of juicer so there is a wrong if [] in juicer.sh when runing juicebox_tools pre job, so it will always run without fragment resolusion.

在 2018年4月8日星期日 UTC+8下午7:49:13，Neva Durand写道：

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/094e3a4b-0ecc-4004-baa6-c898fafe2e57%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

[feng...@gmail.com]

I also get the same report Not including fragment map,so could you tell me which line of the code cause the problem?thank you .

在 2018年4月22日星期日 UTC+8下午10:50:36，shen Eric写道：

[Neva Durand]

Check the help message when you run Juicer. We now by default do not include fragment maps in the HiC file but you can turn it on. 

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/33fcd53e-b992-4b6f-9059-d456bdf933e2%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

[shen Eric]

You can update your juicer.sh script, this may solve the problem.


在 2018年4月23日星期一 UTC+8下午6:27:23，feng...@gmail.com写道：