Extracting read counts from bam file for CDF calculation

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6.8 years ago

phdbiochemist • 0

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

next-gen RNA-Seq • 1.2k views

ADD COMMENT • link 6.8 years ago by phdbiochemist • 0

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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

ADD REPLY • link 6.8 years ago by phdbiochemist • 0

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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 REPLY • link 6.8 years ago by WouterDeCoster 47k

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