[Genome] Inquire about Genome Browser

[Hiram Clawson]

Good Morning Yanwen:

Please note, this CTCF example you mention can be displayed if the data is
transformed into variableStep format.  The following simple shell script
can transform this data:
#!/bin/sh

S=CTCF-summary.graph
R=CTCF-summary.variableStep.txt
rm -f ${R}
head -45 ${S} | egrep "^browser|^track" > ${R}
grep "^chr" ${S} | cut -f1 | sort -u > chr.list
cat chr.list | while read C
do
     echo "variableStep chrom=${C} span=400" >> ${R}
     awk '{if (match($1,"^'"${C}"'$")) { print } }' ${S} | sort -k2n | awk '
{
         printf "%d\t%g\n", $2, $4
}
' >> ${R}
done

This transformation is possible because these data points all happen to be 400
bases wide.  I don't know if the other data sets have this consistent width,
but if they are consistently the same width, they can be transformed into
this variableStep format and will then show all data points in the genome browser.

For example, this CTCF data transformed can be loaded into a custom
track from this URL:
	http://genome-test.cse.ucsc.edu/~hiram/Zhao_et_al/CTCF-summary.variableStep.txt

--Hiram

Yanwen Jiang wrote:
> To whom it may concern:
> 
> This is Yanwen from The University of Chicago.
> 
> We were using your Genome Browser to visualize the data published by Dr.
> Zhao's group at NIH (
> http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/hgtcell.html).  When we were
> directed to the Genome Browser webpage from his paper webpage, we found that
> we couldn't view any data beyond Chr6 for the CTCF data track.  We tried to
> solve this problem by downloading the BED file from his webpage and
> uploading it to your browser manually, but encountered the same problem.  We
> are wondering whether there is a size limitation since we observed the same
> problem for other data tracks that published on his webpage.  We hope we
> could get an answer from you.
> 
> Thanks a lot!
> Yanwen
> 
> Yanwen Jiang
> LeBeau Lab
> The University of Chicago
> ywjiang at uchicago.edu
> 773-702-9164