tab-delimited file - use in bedtools?
Hi,
I have a tab-delimited .txt file. However, instead of being arranged in columns the values appear like so:
Loci ID Lung proportion Heart proportion Kidney proportion^Mloc.40699281 51.70969181 15.88331538^Mloc.14331 5.255465101 86.04853954 8.695995364^M
The ^M seems to indicate where a new line should appear.
I then want to use this file for bedtools intersect with another bedfile containing the locus identities. Is this possible?
Thank you,
1 answer
Hi a.rex,
The ^M is a representation of DOS' carriage return character. Just run dos2unix on that file. Since the data is not in bed-format, try to use join (here are some nice examples: https://shapeshed.com/unix-join/ and http://www.thegeekstuff.com/2012/10/15-linux-split-and-join-command-examples-to-manage-large-files/ ) .
Cheers,
Michael
• 0 views
•
link
written
by
michael.ante
Log in to answer this question.
Which operating system do you use? Did you prepare this file using a Windows program? Looks like a incorrect newline character. I'm not sure if it will help but you could try dos2unix (it often does work)