BEDOPS bedmap confusing file for option
Hi,
I’ve been trying to construct a for loop for getting mean methylation values across certain genomic features but for some reason bedmap is assuming my reference file is an option which makes no sense. My for loop is seen below and I just can’t get it to work.
bed={directory for data files}
map={reference map file}
for region in $map/*.bed;
do
for f in *.bed;
do
awk '{print $1 "t" $2 "t" $3 "t" "-" "t" $4}' $f |
sed '1d' |
bedmap --echo --mean ${region} ${bed}/${f} - > $bed/${f}_results.bed;
done
done
However in my command line I keep getting the error
Error: Option “reference_filename” does not start with ‘–‘
Can anyone guide me on why this is happening when clearly –echo and –mean are the options.
Thank You!
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