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.. _bed12tobed6:
###############
*bed12tobed6*
###############
**bed12ToBed6** is a convenience tool that converts BED features in BED12 (a.k.a. "blocked" BED
features such as genes) to discrete BED6 features. For example, in the case of a gene with six exons,
bed12ToBed6 would create six separate BED6 features (i.e., one for each exon).
==========================================================================
Usage and option summary
==========================================================================
Usage:
::
bed12ToBed6 [OPTIONS] -i <BED12>
=========================== ===============================================================================================================================================================================================================
Option Description
=========================== ===============================================================================================================================================================================================================
**-i** The BED12 file that should be split into discrete BED6 features. *Use "stdin" when using piped input*.
=========================== ===============================================================================================================================================================================================================
==========================================================================
Default behavior
==========================================================================
Figure:
::
head data/knownGene.hg18.chr21.bed | tail -n 3
chr21 10079666 10120808 uc002yiv.1 0 - 10081686 1 0 1 2 0 6 0 8 0 4 528,91,101,215, 0,1930,39750,40927,
chr21 10080031 10081687 uc002yiw.1 0 - 10080031 1 0 0 8 0 0 3 1 0 2 200,91, 0,1565,
chr21 10081660 10120796 uc002yix.2 0 - 10081660 1 0 0 8 1 6 6 0 0 3 27,101,223,0,37756,38913,
head data/knownGene.hg18.chr21.bed | tail -n 3 | bed12ToBed6 -i stdin
chr21 10079666 10080194 uc002yiv.1 0 -
chr21 10081596 10081687 uc002yiv.1 0 -
chr21 10119416 10119517 uc002yiv.1 0 -
chr21 10120593 10120808 uc002yiv.1 0 -
chr21 10080031 10080231 uc002yiw.1 0 -
chr21 10081596 10081687 uc002yiw.1 0 -
chr21 10081660 10081687 uc002yix.2 0 -
chr21 10119416 10119517 uc002yix.2 0 -
chr21 10120573 10120796 uc002yix.2 0 -
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