Entering edit mode
8.7 years ago
bioguy24
▴
230
I am using:
bedmap --echo --skip-unmapped --delim '\t' --echo-map-id-uniq sort_3column_xgen_targets.bed sort_gene.bed > answer.bed
answer.bed
chr1 957570 957852
NOC2L
chr1 976034 976270
PERM1
chr1 976542 976787
PERM1
Is there a way that using that command answer.bed can look like (entries on one line):
answer.bed
chr1 957570 957852 NOC2L
chr1 976034 976270 PERM1
chr1 976542 976787 PERM1
Using Ubuntu 12.0.4 and opening the file in gedit. Thank you.
Yes the bed was an excel document and it looks like I will need to use dos2unix or awk to apply a fix. Thanks :).
Something like this maybe
You can also use sed:
Instead of fixing the output, you might first take a look at your input files and fix those. Either way, it looks like you have some bad characters coming in from Excel, before you use BEDOPS.
Thank you very much :).