HELP: How to generate net track annotation file from the net file?
Zhibo Ma
Hi,
I have generated some net files from two species following the methods you described on in chain and net tracks. But I am having some difficulties to add these net files as custom tracks into the genome Browser.
I am wondering if you could share the tool/scripts you used to generate the net track annotation file for the net tracks from the net file.
Really appreciate!
Zhibo Ma
Zhibo Ma
Graduate student
Department of Cellular Biology
University of Georgia
Athens, GA 30605
Cath Tyner
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Zhibo Ma
On Jan 19, 2018, at 11:44 AM, Cath Tyner <ca...@ucsc.edu> wrote:
Hi Zhibo,
This is a great question! To move forward, please note that the UCSC Genome Browser support team requires that all new and follow-up questions be posted to one of our support forums. In order to best assist you, could you please post your question to one of the forums listed below?
The benefit of posting the question is that our entire support team, including engineers with various expertise, will see your question and we will be able to provide the best support to you. The UCSC Genome Browser support team will look forward to helping you further once your question is posted!
* Confidential/private help: Emailgenom...@soe.ucsc.edu
CathCath Tyner
. . .
UCSC Genome Browser, Software QA & User SupportUC Santa Cruz Genomics Institute
On Thu, Jan 18, 2018 at 1:54 PM, Zhibo Ma <mzh...@uga.edu> wrote:
Hi Cath,
Thanks for your help and suggestions.
I did some research and feel build a minimum local mirror probably is the best solution. I saw the hgLoadNet tool in the kent tree. So I tried and was able to set-up a local mirror of UCSC genome browser on my laptop. It worked fine with mirroring selected small genomes. But I encountered some problem when I try to make the jkweb.a library from kent/src/lib. This library file is needed to compile the hgLoadSqlTab tool.
Compiling hgLoadSqlTab tools requires jkhgap.a and jkweb.a library. I was able to get the jkhgap.a library from kent/src/hg/lib. However, when I try to make the jkweb.a library from the kent/src/lib, it throws me an error:
gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/include/libpng12 -o uuid.o -c uuid.c
In file included from uuid.c:9:0:
../inc/uuid.h:8:23: fatal error: uuid/uuid.h: No such file or directory
compilation terminated.
../inc/common.mk:371: recipe for target 'uuid.o' failed
make: *** [uuid.o] Error 1And I downloaded the newest kent tree file from here: wwwhgdownload.cse.ucsc.edu/admin/jksrc.zip
Could you help me figure out what I can do to make it right?
Really appreciate!
Zhibo
Graduate Student