Sort Bed files

[labrazil]

I think one of the lagging steps is overlapping biofeatures with SNPs. I think it can speed up if we sort the bed files before doing the overlap.

[suhnrhie]

I downloaded the bed files from ENCODE, and what is available for us from ENCODE is one bed file for each biofeature. They combined replicates into one bed file. We cannot get a bed file for each replicate. Is there any way to sort one bed file and remove the overlap region?

[labrazil]

It's not described in the 'name' column of the bed file?

-Houtan

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Houtan Noushmehr, PhD
University of Southern California
http://epigenome.usc.edu/*
*[email protected]
*[email protected]://mail.google.com/mail/?view=cm&fs=1&tf=1&to=[email protected]
*
310.570.2362

On Fri, Nov 18, 2011 at 5:20 PM, suhnrhie <
[email protected]

wrote:

I downloaded the bed files from ENCODE, and what is available for us from
ENCODE is one bed file for each biofeature. They combined replicates into
one bed file. We cannot get a bed file for each replicate. Is there any way
to sort one bed file and remove the overlap region?

---

Reply to this email directly or view it on GitHub:

#19 (comment)

[suhnrhie]

It is not described. >,<

15:04:54 suhn@coetzeeseq CTCF > head
wgEncodeBroadHistoneHmecCtcfStdPk.broadPeak
chr22 16166520 16166725 . 433 . 11.884510 2.0 -1
chr22 16846111 16870502 . 310 . 4.703732 14.0 -1
chr22 16849981 16850304 . 535 . 17.828438 15.7 -1
chr22 16850585 16851031 . 766 . 31.285864 100.0 -1
chr22 16851147 16851383 . 600 . 21.585310 15.7 -1
chr22 16851706 16851854 . 640 . 23.944222 9.7 -1
chr22 16851975 16852159 . 539 . 18.055765 7.1 -1
chr22 16855988 16856101 . 566 . 19.600359 3.1 -1
chr22 16856674 16856802 . 556 . 19.033786 3.9 -1
chr22 17264789 17265078 . 703 . 27.589709 15.7 -1

On Fri, Nov 18, 2011 at 2:13 PM, Houtan <
[email protected]

wrote:

It's not described in the 'name' column of the bed file?

-Houtan

---

Houtan Noushmehr, PhD
University of Southern California
http://epigenome.usc.edu/*
*[email protected]
*[email protected]<
https://mail.google.com/mail/?view=cm&fs=1&tf=1&[email protected]>
*
310.570.2362

On Fri, Nov 18, 2011 at 5:20 PM, suhnrhie <
[email protected]

wrote:

I downloaded the bed files from ENCODE, and what is available for us from
ENCODE is one bed file for each biofeature. They combined replicates into
one bed file. We cannot get a bed file for each replicate. Is there any
way
to sort one bed file and remove the overlap region?

---

Reply to this email directly or view it on GitHub:

#19 (comment)

---

Reply to this email directly or view it on GitHub:

#19 (comment)