I have the results of my first few experiments, and aligned them to my genome etc, but now I would like to count the number of reads I get in a user-defined set of regions.
I am reading about Bedtools and it seems to me that I should be able to use bedtools intersect to obtain this information, does this seem the right way to go?
For example, I have my genome alignment file (as a bam file or summarised into bed/bedgraph), and I want to divide the whole genome into fragments flanked by the motif GATC. I will generate a bed file with the coordinates of every "inter-GATC" fragment, and then I want to ask how many reads I get per fragment. Is bedtools intersect the way to do it? Or are there better ways?
I'm completely new to this, as you may have guessed... just trying to get my head around all the tools available.
Thanks for your help.
I am reading about Bedtools and it seems to me that I should be able to use bedtools intersect to obtain this information, does this seem the right way to go?
For example, I have my genome alignment file (as a bam file or summarised into bed/bedgraph), and I want to divide the whole genome into fragments flanked by the motif GATC. I will generate a bed file with the coordinates of every "inter-GATC" fragment, and then I want to ask how many reads I get per fragment. Is bedtools intersect the way to do it? Or are there better ways?
I'm completely new to this, as you may have guessed... just trying to get my head around all the tools available.
Thanks for your help.
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