bedtools intersect - problem with chromosomes with number >=10?

[Phlya]

Hi!

I have an alignment (.bam) of reads to mm9 genome. I sorted it with samtools sort, so that later I can use -sorted key with bedtools. I also created a .bed-file with regions of interest, in which I want to count number of reads, that mapped to them, and sorted it with command-line sort. I tried this: converted .bam to .bed with bedtools bamtobed and then intersected them counting number of reads:

bedtools intersect -a regions_of_interest.bed -b alignment_sorted.bed -c -sorted  > Neg2H_counts.bedgraph

The problem is, it looks fine for all chromosomes with numbers from 0 to 9 (and X), but all counts for all regions of interest of chromosomes with higher number (chr10, chr11, etc) are 0. There is no biological reason for that, in fact the highest signal should be on chr11. What could be wrong here? I am fairly new to all these tools.

UPDATE
I tried to do the same intersection with bedmap and the result is identical... So there probably is something wrong with my files - what could it be?
I also tried sorting the alignment-derived bed-file in the same way, as I did with the files with regions of interest and it doesn't help.

[blancha]

It could be that the sorting order is not correct in one, or both of the files.
You could just check the chromosomal order in both your BED files.
You could also try the following sort command on both BED files.

sort -k1,1 -k2,2n regions_of_interest.bed > regions_of_interest_sorted2.bed
sort -k1,1 -k2,2n alignment_sorted.bed > alignment_sorted2.bed
bedtools intersect -a regions_of_interest_sorted2.bed -b alignment_sorted2.bed -c -sorted  > Neg2H_counts_sorted2.bedgraph

[Phlya]

Thank you! It seems that it doesn't expect the file to be sorted as chr1, chr2, chr3, but rather as chr1, chr10, chr11, etc. I was sorting them to get the first, logical order, but after sorting as you suggested it worked!