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orphancode / NuMap

NuMap - http://www-hsc.usc.edu/~valouev/NuMap/NuMap.html
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Question about phasogram. #1

Open chesterlee7246 opened 4 years ago

chesterlee7246 commented 4 years ago

Hi! Afrendeiro! I am using NuMap to produce phasogram. There are two files called phasogram:

  1. ./MNase_seq_analysis/dist_plots/whole_genome/phasogram.txt

0 12820795 3114419 853573 278341 107954 48396 24547 13807 8335 5394 1 1111629 127372 24178 7256 2972 1474 875 589 411 313 2 626459 54985 8151 2131 879 442 295 207 153 138 3 569754 50311 7592 2061 834 437 278 199 152 131 4 540173 45549 6610 1726 702 386 255 188 144 117

  1. ./MNase_seq_analysis/dyad_calls/phasogram

0 0 1 0 2 0 3 0 4 0 ... 2996 21487 2997 21319 2998 21379 2999 21075 3000 21159

I am confused about this. Why "./MNase_seq_analysis/dist_plots/whole_genome/phasogram.txt" have 10 columns? What is the difference between these two files? Thanks!

afrendeiro commented 4 years ago

Hi @chesterlee7246, I'm not the author of the software but simply uploaded it for the sake of preservation.

I would need to see the commands you used, but I think that /MNase_seq_analysis/dist_plots/whole_genome/phasogram.txt would be a phasogram of the sequenced reads/fragments. That is used to estimate the average insert size of the library.

I think ./MNase_seq_analysis/dyad_calls/phasogram is a phasogram of dyad calls (the center of the positioned nucleosomes).