Differing number of BED fields encountered at line: 2. Exiting...

[Adrian Johnson]

Hi aaron,
I have the following error:

Differing number of BED fields encountered at line: 2. Exiting...

intersectBed -a myfile.bed -b genesymbols.bed

(columns in myfile.bed : A, T, G, and C refers to frequencies of bases
at that position. white space means 0 reads. First row, there are 5
reads with G and 2 reads with C. A and T are not present.

chrom from to A T G C
chr20 56105555 56105556 5 2
chr20 53100900 53100901 1
chr20 1406258 1406259 5
chr20 28194670 28194671 2 3

genesymbol.bed

chrom from to frm genesymbol
chr1 67075923 67076067 - WDR78
chr1 67078739 67078942 - WDR78
chr1 67085754 67085949 - WDR78
chr1 67100417 67100573 - WDR78
chr1 67109640 67109780 - WDR78
chr1 67113051 67113208 - WDR78

intersectBed -a myfile.bed -b genesymbols.bed

Differing number of BED fields encountered at line: 2. Exiting...

Thats the error.

Does this mean the myfile.BED has white spaces and it is not accepted.
Is there a way to bypass this error.

thanks
Adrian

[Adrian Johnson]

here my aim is to have :

(For example)
chr20 56105555 56105556 5 2 SRC
chr20 53100900 53100901 1 SYK
chr20 1406258 1406259 5 EGFR
chr20 28194670 28194671 2 3 TGFB

I was doing:

intersectBed - a myfile.bed -b genesymbol.bed -wa -wb | cut -f1,2,3,4,5,6,7,12

thanks
Adrian

[Aaron Quinlan]

Hi Adrian,
Is it not possible to use a zero instead of whitespace for a lack of reads? I think this will solve your problem.

Aaron