carandraug
commented
7 years ago I see that you already changed the text to "The modal location of annotated stem-loops is 35 to 50 bp after the stop codon [...]"
I just want to check exactly what coordinate that \StemLoopStart{} and \StemLoopEnd{} are reporting. The code says that the value reported is the mode = most common value.
Yes, that is correct. It is computing the most common distance between the end of the CDS and the start of the stem loop. Since all stem-loops have the same length, we could drop the value of StemLoopEnd altogether and make this simpler?
Here's a table of all distances and counts for each:
| distance from CDS | Number of transcripts |
|---|---|
| 22 | 2 |
| 23 | 1 |
| 24 | 1 |
| 26 | 3 |
| 27 | 3 |
| 28 | 1 |
| 29 | 2 |
| 30 | 5 |
| 31 | 2 |
| 32 | 1 |
| 33 | 4 |
| 34 | 2 |
| 35 | 6 |
| 36 | 3 |
| 37 | 2 |
| 39 | 4 |
| 40 | 2 |
| 41 | 1 |
| 43 | 1 |
| 44 | 3 |
| 46 | 4 |
| 47 | 1 |
| 48 | 1 |
| 49 | 2 |
| 50 | 1 |
| 56 | 1 |
| 57 | 1 |
| 62 | 1 |
| 67 | 2 |
Could we rename the functions to \StemLoopStartMode{} etc,
Done.
and also have \StemLoopStartMin{} and \StemLoopStartMax{}?
Done.
The broader point was that Kevin thought we might have taken the logo/values from elsewhere without citing!
The values have a grey background colour which should have suggested that they were computed automatically. I would say that to be the problem. I was told that it is not obvious that grey background means automatically computed and we should make a bigger scene of this earlier on the manuscript (near the end of the introduction seems to mean most readers will skip it).
aflaus
In the transcript section the calculated value show the stem-loop is from 35-50 bp after the stop codon. The logo shows that the stem-loop is 16 bp long. Our text therefore implies EVERY gene has the stem-loop EXACTLY from 35-50 bp after the stop codon.
I just want to check exactly what coordinate that \StemLoopStart{} and \StemLoopEnd{} are reporting. The code says that the value reported is the mode = most common value.
Could we rename the functions to \StemLoopStartMode{} etc, and also have \StemLoopStartMin{} and \StemLoopStartMax{}? This looks trivial to code since you have the array of values.
NB The broader point was that Kevin thought we might have taken the logo/values from elsewhere without citing! If we state something a little more informative then it makes us look cooler ...