[fabio25]

by fabio

hi zee
thanks for your answer. I was thinking like you at the beginning and so I took the track in the USCS browser and I brought it galaxy. If you do that with a bed file already present in the USCS browser it worked fantastically, but since that the wiz file is in compressed format, Galaxy didn't allow me to do the same actions. I tried to intersect my track with the info in the USCS browser, in order to include more informations in the file, but it still didn't work. And so, I thought that probably there are better ways how to deal this problem. That's why I'm asking to everybody how they analyze the data and if there is any comprehensive suite available to deal with such data.
The other point is that I got them already analyzed and I would like to learn how to preprocess & analyze them. Probably I'm trying to do too many things in one time and I'm getting confused.

[dcfargo]

I'd bring down the entire GFF file from UCSC FTP downloads and then just run a shell script by chromosome with something like

File1 = chr locations
File2 = GFF file

awk '
NR==FNR{
a[NR]=$0
next
}
{
for(i=1;i<NR;i++)
if (a[i] > $4 && a[i] < $5) print $2,$3, "falls between", $4 "and", $5 "at location", a[i]
}
' File1 File2 > Outfile_Chr1 &

Then you can egrep out the fields of interest from the Outfiles.

[sameet]

Hi all,
In the same vein as this post I have one question. I have done peak finding using MACS for a chip-seq experiment. I have the genomic locations of the peaks. Is there a way to find out the location of nearest gene(s) on each side of the location? How easy or difficult is it? I dont think it will be very difficult, but is such a tool already available?

[Thomas Doktor]

You could use BEDTool's closestBed to locate the closest genomic feature. It can be downloaded here: http://code.google.com/p/bedtools/

[sameet]

@ThomasDoktor, thank you for the pointer. It does seem useful.