How to use bedtools to calculate number of reads in windows

Question

[Dacheng]

Hi I want to calculate how many reads from a BAM file (150bp paired end illumina) are in each 20kb non-overlapping windows across the genome. I have constructed the bed files of 20kb windows using bedtools makewindows. I am using bedtools intersect to calculate the number of reads from the bam files. Here is the exact command that I use:

bedtools intersect -a myBAMfile  -b my bedfile of 20kb windows  -c -bed  > output.bed  

I used - c to output the counts and -bed to force output a bed file basically. I wanted some result like this

chr  start end counts 

1      a      b     n

however  the results output was a huge (45GB) file that looks something like this 
1       9999    10047   HWI-ST208:510:C2PKUACXX:1:1307:7971:38840/2     0       +       9999    10047   0,0,0   1       48,     0,      0
1       10000   10051   HWI-ST208:510:C2PKUACXX:1:1101:10183:165157/2   0       +       10000   10051   0,0,0   1       51,     0,      0
1       10001   10052   HWI-ST208:510:C2PKUACXX:1:1105:4675:14114/2     0       +       10001   10052   0,0,0   1       51,     0,      0
1       10001   10052   HWI-ST208:510:C2PKUACXX:1:2108:19598:121982/1   0       +       10001   10052   0,0,0   1       51,     0,      0
1       10002   10053   HWI-ST208:510:C2PKUACXX:1:1302:15349:25257/2    0       +       10002   10053   0,0,0   1       51,     0,      0
1       10003   10054   HWI-ST208:510:C2PKUACXX:1:1104:15953:82940/2    0       +       10003   10054   0,0,0   1       51,     0,      0
1       10003   10054   HWI-ST208:510:C2PKUACXX:1:1306:9147:59251/1     0       +       10003   10054   0,0,0   1       51,     0,      0
1       10004   10055   HWI-ST208:510:C2PKUACXX:1:1202:10485:85215/1    0       +       10004   10055   0,0,0   1       51,     0,      0
1       10004   10054   HWI-ST208:510:C2PKUACXX:1:1303:7159:34459/2     0       +       10004   10054   0,0,0   1       50,     0,      0
1       10004   10039   HWI-ST208:510:C2PKUACXX:1:2103:9398:104872/2    0       +       10004   10039   0,0,0   1       35,     0,      0

Can anyone tell me what I went wrong using bedtools?

[Dacheng]

Hi sorry this is the output I have from running my command

Answer 1

[Pierre Lindenbaum]

switch -a and -b

bedtools intersect -a my.bed  -b my.bam -c   > output.bed  

[Dacheng]

This is counting the times bed files are present in the BAM files? It only gives me zero at the end at all windows

[Pierre Lindenbaum]

check the intervals, check the chromosome notation (chr1 vs 1)