Counting number of base pairs and features in each bed file

Question

[Ron]

Hello all,

Is there any way to count the number of base pairs in each individual bed file?

I know we can do this for the intersecting bed files,but want to to do this separately .

bedtools intersectBed -a file1.bed -b file2.bed -wo

below is the output from the two bed files using intersect and counting number of base pairs from that. However i also want to count the number of total base pairs in each of those bed files too.(per interval and then can sum those up)

chr1  69028   69391   ref|OR4F5,ref|NM_001005484,ens|ENST00000335137,ccds|CCDS30547   chr1    69090   70008   301
chr1  69432   69630   ref|OR4F5,ref|NM_001005484,ens|ENST00000335137,ccds|CCDS30547   chr1    69090   70008   198
chr1  69677   69961   ref|OR4F5,ref|NM_001005484,ens|ENST00000335137,ccds|CCDS30547   chr1    69090   70008   284
chr1  621055  622013  ref|OR4F3,ref|OR4F29,ref|OR4F16,ref|NM_001005221,ref|NM_001005224,ref|NM_001005277,ens|ENST00000440200,ens|ENST00000332831,ccds|CCDS41221   chr1    621095  622034  918
chr1  861071  861574  ref|SAMD11,ref|NM_152486,ens|ENST00000420190,ens|ENST00000342066,ens|ENST00000598827,ens|ENST00000437963,ccds|CCDS2 chr1    861321  861393  72
chr1  865582  865885  ref|SAMD11,ref|NM_152486,ens|ENST00000420190,ens|ENST00000342066,ens|ENST00000598827,ens|ENST00000341065,ens|ENST00000437963,ccds|CCDS2 chr1    865534  865716  134
chr1  866331  866507  ref|SAMD11,ref|NM_152486,ens|ENST00000420190,ens|ENST00000342066,ens|ENST00000598827,ens|ENST00000341065,ens|ENST00000437963,ccds|CCDS2 chr1    866418  866469  51
chr1  871064  871262  ref|SAMD11,ref|NM_152486,ens|ENST00000420190,ens|ENST00000342066,ens|ENST00000341065,ccds|CCDS2 chr1    871151  871276  111
chr1  874294  874969  ref|SAMD11,ref|NM_152486,ens|ENST00000420190,ens|ENST00000342066,ens|ENST00000455979,ens|ENST00000341065,ccds|CCDS2 chr1    874419  874509  90
chr1  874294  874969  ref|SAMD11,ref|NM_152486,ens|ENST00000420190,ens|ENST00000342066,ens|ENST00000455979,ens|ENST00000341065,ccds|CCDS2 chr1    874654  874840  186
  

Thanks

Ron

[Ram]

Can you give us a few sample lines of input and expected output? I don't understand what you mean by counting base pairs and features in a file that contains just contig names and coordinates.

[Ron]

Hi RamRS, I updated my question. I just want to look at the number of base pairs in each bed files.(not features, i Updated it)

[Ram]

It's a tab separated file, you can simply pass the intersect result through awk and have it do $3 - $2 +1 for the first file and $7 - $6 + 1 for the second file, printing each sum out in a new column.

[Ron]

For calculating the total base pairs in each file,shouldn't I calculate the difference in the individual files ? or the intersect result ?I did both ways and the results are different.

[Ram]

If you wish to calculate total base pairs in each file, declare 2 variables in the BEGIN block and add the $3 - $2 +1 to one variable and $7 - $6 + 1 to the other variable in each line, then print them out in the END block (or however you wish to output them)

[Ron]

A follow up question - I also want to count the percentage of UTR's ,exons in my bed file ,so the way would be downloading a bed file for both of them separately(UTR's ,exons) and doing the intersect with the complete bed file of interest?