Question: error with bedtools slop
0
gravatar for Samad
5.0 years ago by
Samad90
France
Samad90 wrote:

Hi, 

I am trying to run a bedtools slop on my.bed file and hg19.genome

bedtools slop -i H3K27me3.bed -g hg19.genome -b 30

I get the following error:

Less than the req'd two fields were encountered in the genome file (genomes/hg19.genome) at line 2.  Exiting.

Any suggestions?

Thanks in advance

Samad

 

chip-seq bedtools • 4.4k views
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Samad90
4
gravatar for Samad
5.0 years ago by
Samad90
France
Samad90 wrote:

The problem was with my hg19.genome file, the correct form has to be as follow (2 columns):

chrom    size
chr1    249250621
chr2    243199373
chr3    198022430
chr4    191154276
chr5    180915260
chr6    171115067
chr7    159138663
chrX    155270560
chr8    146364022

....

To create a new hg19.genome from ucsc, use this: 

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e "select chrom, size from hg19.chromInfo"  > hg19.genome

Thank you for the suggestions

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Samad90
2
gravatar for Alex Reynolds
5.0 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

You might also try bedops --range, which doesn't require any genome table, e.g.:

$ bedops --range 30 --everything H3K27me3.bed > answer.bed
ADD COMMENTlink modified 3.7 years ago • written 5.0 years ago by Alex Reynolds28k
0
gravatar for PoGibas
5.0 years ago by
PoGibas4.8k
Vilnius
PoGibas4.8k wrote:

<Deleted as OP edited his question>

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by PoGibas4.8k

Sorry, I just forgot to put "-g" in my post, the error comes with :

bedtools slop -i H3K27me3.bed -g hg19.genome -b 30

Thank you

ADD REPLYlink written 5.0 years ago by Samad90

Post example of your genome file.

ADD REPLYlink written 5.0 years ago by PoGibas4.8k

I followed steps from the link: http://bedtools.readthedocs.org/en/latest/content/tools/slop.html

hg19.genome is compressed and containing files: cytoBand.txt, hg_alias.tab, proprety.txt and refGene.txt

 

 

ADD REPLYlink written 5.0 years ago by Samad90
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