Extracting read counts from bam file for CDF calculation
Hi, I need some help if possible. I have nascent RNA-seq data (bam files) and would like to calculate an average CDF (cumulative distribution function) of reads downstream of the TSS, say from +1 to +500. I have no idea how to extract this information from a bam file. Once I get that I think I can use the ecdf function in R.
Thanks, Brian
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I'm sorry. I should add more detail about what I want to extract. I need the total counts for each nucleotide, from +1 to +500, which I should be able to use in R using ecdf.
Brian
Please choose a more descriptive title for your thread. "Principal Investigator and beginning bioinformaticist" doesn't say anything about the content of your question.