increase window size

[GoogleCodeExporter]

HI,
I am working with TFBS and want to make false set of TFBS by extending its 
range (window size) in bed format: I could not find a proper bed command that 
will extend the window size and save the output in bed format too. How can I 
tackle problem? Is there any alternative way? Thanks in advance.
regards,
sandesh 

Original issue reported on code.google.com by sandesh....@gmail.com on 27 Sep 2013 at 7:06

[GoogleCodeExporter]

http://bedtools.readthedocs.org/en/latest/content/tools/slop.html

Original comment by aaronqui...@gmail.com on 27 Sep 2013 at 7:09

[GoogleCodeExporter]

Hi, I tried this, it works But I would like to same this change in original bed 
file or  new one. example in this case:

$ cat A.bed
chr1  5   100
chr1  800 980

$ cat my.genome
chr1  1000

$ bedtools slop -i A.bed -g my.genome -b 5000
chr1  0   1000
chr1  0   1000

I would like to save the new values for A or in new.Bed file.

Original comment by sandesh....@gmail.com on 27 Sep 2013 at 7:16

[GoogleCodeExporter]

bedtools slop -i A.bed -g my.genome -b 5000 > new.bed

Original comment by aaronqui...@gmail.com on 27 Sep 2013 at 7:17

[GoogleCodeExporter]

Thank you, I was looking for this.

Original comment by sandesh....@gmail.com on 27 Sep 2013 at 7:23