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r.mulder01
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@rmulder01-23507
Last seen 4.0 years ago
Hi,
Could someone please provide some guidance in reading and anlysing a BED-file using RSAMTOOLS. I needs for each base position a nucleotide frequency. I tried this for a couple of positions (200) which worked, but I now want to scale this up to the complete BED-FILE (appr 160.000 positions). I created the same csv file as for the 200 positions and ran the same script, which seems to work. However I did not get any result even after running it for 3 days. So, it might take longer or there are limitation in r-studio or in RSAMTOOLS, I am not sure. Does anyone have experience with reading and running BED-FILE through RSAMTOOLS.
Hope to hear from you asap.
Kind regard,
René
You would have to show some code. I don't know of any functionality in Rsamtools for reading BED files. It's primarily intended for reading BAM files, which aren't the same thing (and which most certainly are not CSV files).
You could also explain what exactly you are trying to do, as it's not clear (to me at least) what you are trying to do.