Binning BED file and counting antisense / sense reads

Question

[Sam]

I am attempting to bin my BED file that contains gene intervals -2k/2k from the TSS. I would like to produce bins that are 1bp each.

After binning I would like to count anti-sense and sense reads independently. The output data I'm looking for is:

GeneID -2000 -1999 -1998 -1997 ...... 0 ...... 1997 1998 1999 2000
SGIP   0.00  0.00  0.00    1          1        0.00 0.00  9   0.00

Where the first column is the GeneID provided, and the numbers after represent the number of read counts (anti-sense / sense) based on bin interval from TSS.

I'm not quite sure how to do something like this. I at first thought it might be as simple as using bedtools makewindows but I'm unsure if this is appropriate. For read counts, I need a tool that is strand specific and capable of counting anti-sense and sense reads. Which tool would work best for this and what are the input files I require?

Answer 1

[Amitm]

hi,

You could skip the step of creating 1bp bins. Just use one line for each 2k window. And then using Bedtools Coverage use parameter -d. That will give depth at each base anyway. Also you can use the -s to force strandedness. Obviously your input BED must have the strand column.

[Sam]

This is great to hear! I'll sort this out today and let you know how it goes so I can accept your answer or ask additional questions.