Question: Extracting read counts from bam file for CDF calculation
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gravatar for phdbiochemist
23 months ago by
phdbiochemist0 wrote:

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

rna-seq next-gen • 610 views
ADD COMMENTlink modified 23 months ago • written 23 months ago by phdbiochemist0

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

ADD REPLYlink written 23 months ago by phdbiochemist0

Please choose a more descriptive title for your thread. "Principal Investigator and beginning bioinformaticist" doesn't say anything about the content of your question.

ADD REPLYlink written 23 months ago by WouterDeCoster39k
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