Problem with Genome file in bedtools complement

[Chudar]

Hi all,

I am new to bedtools. I want to use the bedtools complement with my bed file to find the regions outside the targets. As I dont have genome file available in the internet available, I deleted the last two columns of samtools faidx output which I used as genome file.

Now when I run the bedtools complement like following

bedtools complement -i sorted_bed_file -g genome.txt

It gave me an error  ". Exiting...teger conversion of string "561146"

Here is the first few lines of the genome.txt

scaffold7446    561146
scaffold5316    433321
scaffold643    429010
scaffold98    422919
scaffold3363    413090
scaffold3212    409136
scaffold2550    407169
scaffold1007    398371
scaffold595    396031
scaffold459    378365
scaffold398    369307
scaffold2228    367210
scaffold3743    366599
scaffold3048    355827

Kindly guide me where the problem lies. Thanks in advance.

Regards

Chudar

[John Marshall]

On 8 Apr 2016, at 15:38, Chudar <chudar...@gmail.com> wrote:
> It gave me an error ". Exiting...teger conversion of string "561146"

That error message is garbled in a way that often indicates that your file (genome.txt) has Windows-style CR-LF line endings but the program isn't expecting them.

John

--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.

[Chudar]

Hi John,

You are right. I corrected my problem, now it works. Thank you very much

Regards
Chudar