Question: bedtools probelm of syntax
0
gravatar for Korsocius
5.0 years ago by
Korsocius150
Korsocius150 wrote:

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

dna map bedtools • 1.3k views
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Korsocius150
3
gravatar for Aaronquinlan
5.0 years ago by
Aaronquinlan11k
United States
Aaronquinlan11k wrote:

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

ADD COMMENTlink written 5.0 years ago by Aaronquinlan11k

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

ADD REPLYlink written 5.0 years ago by Korsocius150
1

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).
ADD REPLYlink written 5.0 years ago by Aaronquinlan11k

It works......

ADD REPLYlink written 5.0 years ago by Korsocius150
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