how to collapse sam/bam to bed with read count

[Joseph Dhahbi, PhD]

Hi
is there a way to combine tools to collapse a bam or sam file into a bed
file with the following columns:
#chr start end id read_count strand

Regards,
Joseph

Joseph M. Dhahbi, PhD
Childrens Hospital Oakland Research Institute
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[Aaron Quinlan]

Hi Joseph,

In this case, what would the ID represent?

Assuming it is meaningless, you could do something like (untested, just whipped together, so caveat emptor):

# step 1. create a bedgraph of the forward strand alignments.
genomeCoverageBed -i <(bamToBed -i aln.bam | awk '$6=="+") -g chrom.sizes -bg > plus.bedg

# step 2. create a bedgraph of the reverse strand alignments.
genomeCoverageBed -i <(bamToBed -i aln.bam | awk '$6=="-") -g chrom.sizes -bg > neg.bedg

# step 3. combine the two bedgraphs, adding a strand and a fake ID
# 3a. use awk to add a strand column
# 3b. sort by chrom and strand
# 3c. add some fake ID which is the line number
(cat plus.bedg | awk '{print $0"\t+"; cat neg.bedg | awk '{print $0"\t-") | \
sort -k1,1 -k2,2n | \
awk '{OFS="\t"; print $1,$2,$3,NR,$4,$5}' \
> joseph.out

I hope this helps.
Aaron