Hello, your videos are really great. However I’m meeting a few hurdles. I’m using my own FASTA files generated after sequencing (illumina platform). For each isolate I have them in contigs. So about 60 contigs or more for each isolate. Could you help out with how to combine the contigs into a single contig so that I can go ahead and do the alignment With Mega or Muscle?
You can perform a reference guided scaffolding using the tool ragtag (github.com/malonge/RagTag). This will generate a consensus sequence, that you can use for the alignment. Also , I recommend the recent videos I made on phylogenetic trees. They may be helpful ua-cam.com/video/NBiBuec2C_8/v-deo.html ua-cam.com/video/dqflfY0jqgQ/v-deo.html ua-cam.com/video/q3DcUCWe_wk/v-deo.html ua-cam.com/video/9SniaKyUGfk/v-deo.html
Thanks for the tutorial. I enjoyed it.
Glad you enjoyed it!
Hello, your videos are really great. However I’m meeting a few hurdles. I’m using my own FASTA files generated after sequencing (illumina platform). For each isolate I have them in contigs. So about 60 contigs or more for each isolate. Could you help out with how to combine the contigs into a single contig so that I can go ahead and do the alignment With Mega or Muscle?
You can perform a reference guided scaffolding using the tool ragtag (github.com/malonge/RagTag). This will generate a consensus sequence, that you can use for the alignment.
Also , I recommend the recent videos I made on phylogenetic trees. They may be helpful
ua-cam.com/video/NBiBuec2C_8/v-deo.html
ua-cam.com/video/dqflfY0jqgQ/v-deo.html
ua-cam.com/video/q3DcUCWe_wk/v-deo.html
ua-cam.com/video/9SniaKyUGfk/v-deo.html
@@bioinformaticscoach
Thanks a lot. I will try that
Can you provide help with tree generation using RAXML
RAXML is on one of my upcoming videos
@@bioinformaticscoach thanks is there a way to connect to you. Please leave me you mail id, mine is rajneesh.dadwal@gmail.com
Yes you can connect with me. Please send me a DM on twitter @bioinfocoach
The RAXML video will be released this week. I just uploaded how you can install it.
The raxml tutorial has been uploaded. ua-cam.com/video/NBiBuec2C_8/v-deo.html
Good Job, but I have a challenge, when I call the python3 draw_phylo.py phyml_tree.txt I get an a error.
Can you post the error message?
Ook sure
Traceback (most recent call last):
File "draw_phylo.py", line 20, in
Phylo.draw(tree,do_show=False)
File "/home/gyrp/share/Sun_28_feb_21/Practice/phylo/lib/python3.8/site-packages/Bio/Phylo/_utils.py", line 501, in draw
fig = plt.figure()
File "/home/gyrp/share/Sun_28_feb_21/Practice/phylo/lib/python3.8/site-packages/matplotlib/pyplot.py", line 687, in figure
figManager = new_figure_manager(num, figsize=figsize,
File "/home/gyrp/share/Sun_28_feb_21/Practice/phylo/lib/python3.8/site-packages/matplotlib/pyplot.py", line 315, in new_figure_manager
return _backend_mod.new_figure_manager(*args, **kwargs)
File "/home/gyrp/share/Sun_28_feb_21/Practice/phylo/lib/python3.8/site-packages/matplotlib/backend_bases.py", line 3494, in new_figure_manager
return cls.new_figure_manager_given_figure(num, fig)
File "/home/gyrp/share/Sun_28_feb_21/Practice/phylo/lib/python3.8/site-packages/matplotlib/backends/_backend_tk.py", line 885, in new_figure_manager_given_figure
window = tk.Tk(className="matplotlib")
File "/home/gyrp/miniconda3/lib/python3.8/tkinter/__init__.py", line 2261, in init
self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: couldn't connect to display "localhost:0.0"Traceback (most recent call last):
File "draw_phylo.py", line 20, in
Phylo.draw(tree,do_show=False)
File "/home/gyrp/share/Sun_28_feb_21/Practice/phylo/lib/python3.8/site-packages/Bio/Phylo/_utils.py", line 501, in draw
fig = plt.figure()
File "/home/gyrp/share/Sun_28_feb_21/Practice/phylo/lib/python3.8/site-packages/matplotlib/pyplot.py", line 687, in figure
figManager = new_figure_manager(num, figsize=figsize,
File "/home/gyrp/share/Sun_28_feb_21/Practice/phylo/lib/python3.8/site-packages/matplotlib/pyplot.py", line 315, in new_figure_manager
return _backend_mod.new_figure_manager(*args, **kwargs)
File "/home/gyrp/share/Sun_28_feb_21/Practice/phylo/lib/python3.8/site-packages/matplotlib/backend_bases.py", line 3494, in new_figure_manager
return cls.new_figure_manager_given_figure(num, fig)
File "/home/gyrp/share/Sun_28_feb_21/Practice/phylo/lib/python3.8/site-packages/matplotlib/backends/_backend_tk.py", line 885, in new_figure_manager_given_figure
window = tk.Tk(className="matplotlib")
File "/home/gyrp/miniconda3/lib/python3.8/tkinter/__init__.py", line 2261, in init
self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: couldn't connect to display "localhost:0.0"
@@nanaamoako5172 Please raise an issue on the github page so that we discuss.
@@bioinformaticscoach Alright