bed12tobed6

bed12tobed6

#convert2bed

#convert2bed --input=gtf [–output=fmt] [options] < input > output

#sort -k 1,1 -k 4,4n gencode.vM1.annotation.gtf > gencode.vM1.annotation.sort.gtf

#convert2bed -i gtf < gencode.vM1.annotation.sort.gtf > mm9.sorted.bed

#python3 bed6Tobed12.py mm9.sorted.bed > mm9.sorted.bed12 ##z这脚本不可信

#convert2bed是BEDOPS软件包里非常常用的函数，可以把常见的二进制或者文本基因组文件（BAM, #GFF, GTF, GVF, PSL, OUT, SAM, VCF，WIG）转换成bed格式。这里的bed格式大部分都是bed6格式。

bed12ToBed6 -i cs12.bed>cs6.bed

bed12ToBed6
在Bedtools 2.8版本中，five bedtools - intersect, coverage, genomecob, bamToBed, and bed12ToBed6 常用来处理bed文件

[ Format conversion ]

bamtobed      Convert BAM alignments to BED (& other) formats.
bedtobam      Convert intervals to BAM records.
bamtofastq    Convert BAM records to FASTQ records.
bedpetobam    Convert BEDPE intervals to BAM records.
bed12tobed6   Breaks BED12 intervals into discrete BED6 intervals.

(rna) yyp@DESKTOP-LRUCLJJ:/mnt/c/Users/admin/Desktop$ bed12ToBed6 -help

*****ERROR: Unrecognized parameter: -help *****

Tool: bedtools bed12tobed6 (aka bed12ToBed6)
Version: v2.30.0
Summary: Splits BED12 features into discrete BED6 features.

Usage: bedtools bed12tobed6 [OPTIONS] -i

Options:
-n Force the score to be the (1-based) block number from the BED12.