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titleclick here to see the bedtools merge code and output
Code Block
languagebash
titlesolution code
bedtools merge -s -c 4,5 -o count_distinct,sum -i yeast_pairedend_sort.mapped.q1.bed > yeast_pairedend_sort.mapped.q1.merge.bed
more yeast_pairedend_sort.mapped.q1.merge.bed
wc -l yeast_pairedend_sort.mapped.q1.merge.bed

#without strand considered
bedtools merge -c 4,5,6 -o count_distinct,sum,distinct -i yeast_pairedend_sort.mapped.q1.bed > yeast_pairedend_sort.noStrand.mapped.q1.merge.bed
Code Block
languagebash
wc -l yeast_pairedend_sort.noStrand.mapped.q1.merge.bed
40319 yeast_pairedend_sort.noStrand.mapped.q1.merge.bed #without the -s option

wc -l yeast_pairedend_sort.mapped.q1.merge.bed
76601 yeast_pairedend_sort.mapped.q1.merge.bed #with the -s option

more yeast_pairedend_sort.mapped.q1.merge.bed 
chrI    219     344     +    2     66
chrI    368     469     -    1     29
chrI    684     785     -    1     37
chrI    871     955     +    6     174
chrI    971     1079    -    7     211
chrI    1216    1322    +    6     157
chrI    1347    1437    -    6     157
chrI    2892    2993    +    14    406
chrI    3010    3111    +    1     37
chrI    3013    3107    -    14    406

more yeast_pairedend_sort.noStrand.mapped.q1.merge.bed
chrI    219     344     2     66     +
chrI    368     469     1     29     -
chrI    684     785     1     37     -
chrI    871     955     6     174    +
chrI    971     1079    7     211    -
chrI    1216    1322    6     157    +
chrI    1347    1437    6     157    -
chrI    2892    2993    14    406    +
chrI    3010    3111    15    443    +,-

Note the change in column order in the first set of commands.  We can use awk like this to change the column order, either piped in the original command or after the fact:

Code Block
languagebash
titleusing awk for column reordering
#after the creation of the first file
cat yeast_pairedend_sort.mapped.q1.merge.bed | awk '{print $1 "\t" $2 "\t" $3 "\t" $5 "\t" $6 "\t" $4}' > yeast_pairedend_sort.mapped.q1.merge.bed

#piped in-line
bedtools merge -s -c 4,5 -o count_distinct,sum -i yeast_pairedend_sort.mapped.q1.bed | awk '{print $1 "\t" $2 "\t" $3 "\t" $5 "\t" $6 "\t" $4}' > yeast_pairedend_sort.mapped.q1.merge.bed


bedtools intersect: identifying where two experiments overlap (or don't overlap)

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