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dincarnato / RNAFramework

RNA structure probing and post-transcriptional modifications mapping high-throughput data analysis
http://www.rnaframework.com
GNU General Public License v3.0
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rf_count frequencies folder #43

Closed dfporter closed 11 months ago

dfporter commented 11 months ago

rf_count produces a subfolder called frequencies with a single file containing each dinucleotide pair, including AA/TT/CC/GG, and a float value, with the floats summing to 1. The perl that makes this is opaque to me, what is the interpretation of this file? Does "AA" represent a deletion of an "A" base?

dincarnato commented 11 months ago

Dear Douglas,

you are right. This should be added to the manual. The frequencies/ folder is generated when rf-count is ran with the -of parameter. It contains the frequency of each base substitution in the experiment. The AA/CC/GG/TT should all be 0, cause it's like saying that the base was substituted by itself.

Important: we noticed over the past 2 weeks that there was a bug causing those frequencies to be miscalculated in the presence of indels. The bug is now fixed and we have already pushed the working version of rf-count, so i would recommend you to do a git pull and rerun your analysis. We have now released RNAFramework v2.8.5.

dfporter commented 11 months ago

Thank you!