All RU (relative usage) values are 1

[matdoering]

Running the recommended workflow with STAR, all RU values end up being 1 using custom data. Implementing the transcriptome re-alignment in addition to the genome alignment unfortunately didn't change things.

Investigating the source code, I found that the reason for RU's being 1 is that there is only always a single segment:

mountainClimber/src/mountainClimberRU.py

Line 234 in 65132f2

write_output_cp_left(o3, gene, this_seg, n=nsamples, ind=ind, ru=1)

Any ideas on how to fix that?

[matdoering]

Setting the param --winsize of mountainclimberCP to a lower value (e.g. 10) seems to help but that leads to other issues, namely:

Traceback (most recent call last):
  File "/mountainClimberCP.py", line 1396, in <module>
    main(sys.argv[1:])
  File "/mountainClimberCP.py", line 1113, in main
    peak_inds_ttest_opt = param2cpopt[(denoise_winsize_opt, amp_thresh_opt, peak_min_dist_opt)].tolist()
KeyError: (10, 0.15, 50)