Problems with deduplicate

Guosong Wang

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Sep 17, 2018, 3:47:56 PM9/17/18

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Hi!

I am a new user of the methpipe and I have only tried to analyze bs-seq with bismark before. I have been following the manual, and I got stuck at the merging and deduplication step, my problem is:

The version of methpipe I downloaded (v3.4.3, I download this from http://smithlabresearch.org/software/methpipe/), there wasn't a duplicate-remover in the bin directory of methpipe, did you remove this program for some reasons or I was looking at the wrong directory?

Thanks for your time and patience!

Best regards,

---

Guosong Wang, Ph.D student

Department of Animal Sicence

Texas A&M University

College Station, TX, 77843

Xiaojing Ji (Liz Ji)

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Sep 19, 2018, 7:53:22 PM9/19/18

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Hi Guosong,

The duplicate-remover should be included. Have you run ``make install'' after the compiling? Also could you send us a screenshot of your bin directory?

Thanks,

Liz

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Xiaojing Ji

Molecular and Computational Biology,

University of Southern California

1050 Childs Way, RRI 408c

Los Angeles, CA, 90089

Guosong Wang

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Sep 20, 2018, 9:37:41 PM9/20/18

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Hi Xiaojing,

Thanks for answering me!

For your first suggestion, since I don't have the permission to install any source code on cluster, the methpipe was installed by the administrator and I strongly suppose he installed it following the installation guide under the website.

And here is a screenshot for the ~/methpipe/bin/ directory:

Screen Shot 2018-09-20 at 8.14.30 PM.png

Again, I truly appreciate your help!

Kind regards,

Guosong

Xiaojing Ji (Liz Ji)

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Sep 22, 2018, 5:53:47 PM9/22/18

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Hi Guosong,

Looks like all binaries from the folder "utils" are missing. Please check if the folder "utils" exists under your "src" directory. If they are present, they might not have been successfully compiled - we will need more information about the compiling process. You may need to contact your administrator to provide the error messages from compiling if any. You may also could try to install the methpipe under your home directory.