sort-bed issue urgent

Question

[tanni93]

Hi all, I have a bed file named input.bed (excel file with three columns: chr#+start+end --> saved as tab-demilitied --> saved as .bed). When I type "sort-bed input.bed > final.bed" I get this error:

BED row length exceeds capacity at line 1 in final.txt.
Check that you have unix newlines (cat -A) or increase TOKENS_MAX_LENGTH in BEDOPS.Constants.hpp and recompile BEDOPS.

I tried trouble-shooting, this is what I got:

$ wc -l input.bed
       0 input.bed
$ head -n input.bed | cat -A
head: illegal line count -- input.bed
cat: illegal option -- A
usage: cat [-benstuv] [file ...]

Any help would be greatly appreciated! I am very close but I need the bigbed formatted files in an hour! Thank you Biostar community!

[apelin20]

since this is so urgent let me drop everything and get right to it. try:

cat -A input.bed | head

PS. Why did you have to post this in different places?

A: bed to bigBed conversion

[tanni93]

This is my output:

cat: illegal option -- A
usage: cat [-benstuv] [file ...]

[tanni93]

Hi Apelin20, I have gotten to the last step --> when I use bedToBigBed I am getting this error:

cannot execute binary file

what does this mean? And what can I do now to run this?

[tanni93]

Hi Apelin20, I have gotten to the last step --> when I use bedToBigBed I am getting this error:

cannot execute binary file

what does this mean? And what can I do now to run this?

[Alex Reynolds]

Did you export from Excel on Windows, or export from Excel on Mac? Either way, you have to fix Microsoft-formatted text files to work in UNIX, but please indicate which and I can tell you what to run to fix the problem.

Answer 1

[Alex Reynolds]

You can do the following in the case of exporting from Excel on Mac:

$ tr '\r' '\n' < input.bed > input.fixedLineEndings.txt

If you exported your data from Excel on Windows:

$ tr -d '\r' < input.bed > input.fixedLineEndings.txt

Then you can sort normally:

$ sort-bed input.fixedLineEndings.txt > final.bed

Then, assuming you have downloaded the correct bedToBigBed binary for your platform, you can convert the resulting BED file to bigBed.

[tanni93]

Hi Alex, This works now! Thank you very much!