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The filling color problem of modified bases after DNA folding
Posted: Fri May 19, 2023 2:48 am
by 541
When you fold the DNA, how do you change the color of each base? At present, only two colors can be modified. How to make different colors? I hope you can tell me the tutorial on how to modify the base color. I am looking forward to your reply. Thank you
Re: The filling color problem of modified bases after DNA folding
Posted: Tue May 23, 2023 6:18 am
by julie_huang
Hi there, I have the similar question.
I hope different colors can be used when visualizing as jpg file.
I have found this option using command line:
Code: Select all
Usage: sir_graph [options] infile[.ct] | infile.ss
-col <color_file> (User supplied color file.)
-col_ann <color_ann_file> (As above for annotation colors)
However, I did not find an example color file or annotation file that goes with the input ".ct" file.
For example, if I have a ".ct" file as below:
Code: Select all
18 dG = 1.768 assay_fp
1 g 0 2 0 1 0 0
2 c 1 3 0 2 0 3
3 g 2 4 10 3 2 4
4 g 3 5 9 4 3 0
5 c 4 6 0 5 0 0
6 g 5 7 0 6 0 0
7 t 6 8 0 7 0 0
8 t 7 9 0 8 0 0
9 c 8 10 4 9 0 10
10 c 9 11 3 10 9 11
11 t 10 12 0 11 10 0
12 g 11 13 0 12 0 0
13 t 12 14 0 13 0 0
14 c 13 15 0 14 0 0
15 t 14 16 0 15 0 0
16 c 15 17 0 16 0 0
17 t 16 18 0 17 0 0
18 c 17 0 0 18 0 0
I plan to highlight the first 5 bases (gcggc) and last 5 bases (ctctc). How do I provide the "-col" color_file, or "-col_ann" file?
I noticed in the webpage version
http://www.unafold.org/mfold/applicatio ... g-form.php
If I provide high-light as "1-5, 14-18", I can get the exact plot I want. I wonder how to do so using the "sir_graph" command line tool.
Thanks!