BED (Browser Extensible Data) Documentation

Here are documentations and tools for making and handling BED file: BED-Ensembl, bedtools-Github and bedtools

An example:

BEDsnippet

BEDsnippet

Intersect bam file with gtf file to obtain a bed file for analysis

bedtools intersect -a xxxxxx.bam -b xxxxxx.gtf -bed -wo > overlaps.bed

number of overlaps reported

wc –l overlaps.bed

number of overlaps 10 bases or longer

cut -f22 overlaps.bed | sort -nrk1 > lengths

cut -f22 overlaps.bed | sort -nrk1 | grep -n “^9” | head -1

number of alignments (from BAM file) overlap the annotations (GTF file)

cut –f1-12 overlaps.bed | sort –u | wc -l

number of exons have reads mapped to them

cut –f13-21 overlaps.bed | sort –u | wc -l

Alternatively, convert BAM to BED format and intersect it with GTF for analysis

bedtools bamtobed -i xxxxxx.bam > xxxxxx.bed

number of overlaps reported

957 bedtools intersect -wo -a xxxxxx.gtf -b xxxxxx.bed | wc -l

number of overlaps 10 bases or longer

959 bedtools intersect -wo -a xxxxxx.gtf -b xxxxxx.bed | cut -f16 > count_base.txt

number of alignments (BAM) overlap the annotations (GTF)

962 bedtools intersect -wo -a xxxxxx.gtf -b xxxxxx.bed | cut -f6 > count_base_1.txt

number of exons have reads mapped to them

967 bedtools intersect -wo -a xxxxxx.gtf -b xxxxxx.bed |cut -f4|sort -u |wc -l

number of bed records created

968 bedtools intersect -wo -a xxxxxx.gtf -b xxxxxx.bed |cut -f9|cut -d " " -f4|sort -u |wc -l

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