BedTools - Stop column appears to be non-numeric
Entering edit mode
5.9 years ago
dearbbhyc • 0

I have just recently downloaded bed-tools and am trying to get the hang of it. My files seem to be in perfect BEDfile format ; yet when I try intersect them it says that there are non-numeric values. So I looked at the d.type via :

cat -e /Users/casey/Documents/Bedfiles/chr1_2.bed | more

and it looks like the last column does have non numerical values that are not showing in my txt file:

\f0\fs24 \cf0 chr1      10169   207666.0\$
chr1    88000   297956.0\$
chr1    258565  358335.0\$
chr1    268963  415287.0\$
chr1    92387   415287.0\$
chr1    287146  477428.0\$
chr1    110582  495598.0\$
chr1    139463  535988.0\$
chr1    357216  733912.0\$
chr1    268963  651035.0\$
chr1    92387   651035.0\$
chr1    286643  712376.0\$
chr1    110079  730504.0\$
chr1    494665  777174.0\$
chr1    139463  777174.0\$
chr1    12788873        12865723.0\$

Is there a way I can change the format of the final column?? Thank you

bedtools • 2.0k views
Entering edit mode

This appears to be a file edited on a PC. If you have dos2unix utility available then run it on this file. Or something along the lines here.


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