error with bedtools slop
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
3 answers
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
You might also try bedops --range, which doesn't require any genome table, e.g.:
$ bedops --range 30 --everything H3K27me3.bed > answer.bed
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Ram
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written
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Alex Reynolds
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Alex Reynolds
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
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