Good Morning Gerd:
Your best bet is to transform this file into a bed file format:
awk '{printf "%s\t%d\t%d\t%s\t0\t%s\n", $5, $6-1, $7, $2, $4}' yourFile.txt
If any of your columns have some kind of relevant score value, transform
it into the range [0-1000] and use it in column 5 where I have a 0
in this example.
--Hiram
----- Original Message -----
From: "Gerd Anders" <[email protected]>
To: [email protected]
Sent: Tuesday, December 28, 2010 3:28:20 AM
Subject: [Genome] Which (file) format for clustered data?
Dear all,
there is a public available data set with clusters of genome-mapped
reads looking
like this:
Cluster: slc1001 5.00 + chr1 89073413 89073444
32 mRNA 1.00 5.00 5
Cluster: slc1001 5.00 + chr7 107347391 107347410
20 mRNA 1.00 5.00 5
Cluster: slc100 5.00 + chr16 8785682 8785709 28 mRNA 1.00
5.00 5
Cluster: slc1007 5.00 - chr15 32421230 32421272
43 mRNA 1.00 5.00 5
Cluster: slc1010 5.00 - chr15 33058221 33058246
26 mRNA 1.00 5.00 5
Cluster: slc1011 5.00 + chr8 107833701 107833732
32 mRNA 1.00 5.00 5
Cluster: slc1012 5.00 - chr16 20716458 20716489
32 mRNA 1.00 5.00 5
Cluster: slc1014 5.00 + chr1 89953251 89953296
46 mRNA 1.00 5.00 5
which is supposed to be added as a local track in our local UCSC Genome
Browser
mirror. I already added a couple of 'easy' BED files as local tracks,
but I have no idea
in which file format such a clustering has to be stored (and how),
whether this is suppor-
ted by the corresponding track.ra file or even not possible. I have been
told that the
UCSC Genome Browser supports a kind of clustering. Do I have to
transform these
data into a BED format or may I ask you to give me any other hint ,
please? Thanks
a lot in advance.
Cheers,
Gerd
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