I used paired-end sequence data for copy number variation study; and eventually get .txt files as output. I'm hoping to use Bedtools to compare my results with others.
Can I convert .txt files into .bed files? (I don't see option in Bedtools)
If Bedtools is not working, what software can I use for data comparison?
my lines of txt is just like:
deletion chr9:6169901-6173000 3100 deletion chr9:7657401-7658800 1400 deletion chr9:8847501-8848600 1100 deletion chr9:10010201-10011600 1400 deletion chr9:10126601-10127700 1100
edit: I converted the txt files into bedpe format, which looks like
chr21 18542801 18543500 chr21 18545701 18545900 chr21 19039901 19040600 chr21 19164301 19169400 chr21 19366001 19370200 chr21 19639601 19640300 chr21 20493701 20495700 chr21 20581401 20583000 chr21 20880901 20882700 chr21 21558601 21559700
Then I started to compare two bedpe, looking for overlapping region, using the command like:
pairToPair -a 1.bedpe -b 2.bedpe > share.bedpe
Then I see the errors:
It looks as though you have less than 6 columns. Are you sure your files are tab-delimited?
MY bed file have only three columns, seems it requires 6....What's the problem here? thx