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Dowell-Lab / FStitch

Fast Stitch Reader (FStitch) -- fast-processing tool written in C for the annotation of regions of active transcription.
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Large differences in LLR calculated values between bedGraph formatted files #4

Open magruca opened 5 years ago

magruca commented 5 years ago

In GitLab by @magr0763 on Sep 28, 2018, 09:42

I performed different iterations of FStitch train using the following bedGraph formats GC uncorrected and corrected on a single sample:

1) bedtools standard out (bt) 2) bedtools 5' (bt5prime) 3) deepTools (dt)

I got markedly different final LLR values for each ranging from the 10^3 to 10^5 as shown in these .hmminfo files:

bt5prime.hmminfo

bt.hmminfo

dt.hmminfo

These values were not significantly different between GC corrected and uncorrected (they were on the same order of magnitude). However, when I ran segment using these training files, I did not get drastically different results. That makes me suspicious of the LLR behavior, but this would probably be better addressed by Robin I imagine.

magruca commented 5 years ago

In GitLab by @magr0763 on Sep 28, 2018, 09:43

changed the description