5.1.4. 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).
5.1.4.1. Usage and option summary¶
Usage:
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- bed12ToBed6 [OPTIONS] -i <BED12>
| Option | Description |
|---|---|
| -i | The BED12 file that should be split into discrete BED6 features. Use “stdin” when using piped input. |
5.1.4.2. Default behavior¶
Figure:
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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 -
