bedtools probelm of syntax

Question

[Korsocius]

Hi I would like to use this syntax, but bedtools has a problem with -f function, do you know where could be a problem pls? ($z is a bam file.....)

bedtools map -a /home/filip/Desktop/binary_NIFTY.bed -b $z -c 10,10 -o count,concat -f | awk -v OFS="\t" 'BEGIN {print "CHR\tSTART\tSTOP.............................

Thank you for help. Filip

Answer 1

[Aaronquinlan]

You need to supply a value for the -f argument. For example, if you require 50% overlap, provide -f 0.05.

[Korsocius]

But there is a default value or not? (for one base 1bp)

[Aaronquinlan]

Yep, default (without providing -f) will detect one base pair. If you use, -f you are trying to override that default, and as such, must provide a value to use as the override.

    -f    Minimum overlap required as a fraction of A.
        - Default is 1E-9 (i.e., 1bp).

[Korsocius]

It works......