Hi,
I have been trying to use bedtools to extract 200bp flanking sequence around my snps
bedtools slop -i snps.v03.bed -g Aradu.len.v02 -b 200
I get this error return instead
Less than the req'd two fields were encountered in the genome file (Aradu.len.v02) at line 2. Exiting.
What required fields is the code complaining about?
Here's a snippet of my genome file
chrom size
Aradu.A01 107035537
Aradu.A02 93869048
Aradu.A03 135057546
Aradu.A04 123556382
Aradu.A05 110037037
And here's the snp file
Aradu.A02 1992401 AX-147212565
Aradu.A02 67418563 AX-147213997
Aradu.A02 67418823 AX-147213999
Aradu.A02 67418874 AX-147214001
Aradu.A02 67420580 AX-147214004
Aradu.A02 79194257 AX-147214308
Can you help with this?
Kind regards,
Paul
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written
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paulotyama •
The problem is with the format.
Genome file should be:
Aradu.A01 107035537
Aradu.A02 93869048
Aradu.A03 135057546
Aradu.A04 123556382
Aradu.A05 110037037
SNP file should be a BED format
Aradu.A02 1992401 1992401 AX-147212565
Aradu.A02 67418563 67418563 AX-147213997
Aradu.A02 67418823 67418823 AX-147213999
Aradu.A02 67418874 67418874 AX-147214001
Aradu.A02 67420580 67420580 AX-147214004
Aradu.A02 79194257 79194257 AX-147214308
You could easily generate that using:
awk -v OFS="\t" '{ print $1,$2,$2,$3}' snps.v03.bed > snps.v03.new.bed
Thanks Goutham,
I still get the same complaint even after I reformat both files as you suggested. Any more ideas?
Thanks again,
Paul
1) @Goutham did not say to reformat both files, only the SNP file. And it would be useful to show us a few lines of the reformatted SNP file for us to validate.
2) Are you sure that your Genome file is tab-delimited? The error message indicates less than two fields. Or the first line (chrom size) could be the problem. Delete it and retest.
Nope, it works perfectly!
I just had to format my genome file with a tab delimiter.
Log in to answer this question.
Can you format your file contents as code (highlight and click on the button with 0s and 1s)? Otherwise, it gets auto-formatted poorly.
It looks like your BED file is not really a BED file. It should start with these 3 columns: chromosome, start, end.
Formatting adjusted.
Thanks Igor.
I reformatted the snp file as BED like you suggested and removed headers from the genome file but I still get the same complaint.
Paul