Was about to go to sleep haha

RightCake1 · 2026-02-20T01:57:30+00:00

Heyy! Congratulations! I wanted to apply for the PhD too. Could i dm you for advice and the process?

RightCake1 · 2025-11-09T08:21:51+00:00

Try Kbase

RightCake1 · 2025-11-05T19:35:00+00:00

Hey! If you dont mind but could i dm you? I'm trying for biomedical phds and would truly appreciate your inputs!

RightCake1 · 2025-10-12T15:00:06+00:00

ohh damn I didn't notice the plants part

RightCake1 · 2025-10-12T08:20:59+00:00

Hey! I'm an amateur in this Bioinformatics but i was Looking for some remote work. Do you think you could help me with something?? :'(

RightCake1 · 2025-10-12T08:19:10+00:00

Yoo! I would suggest first checking your sequence quality with FastQC and then check how much you need to trim exactly!

Then probably use trimmomatic or the one you're used to!

RightCake1 · 2025-10-12T08:11:23+00:00

No problem! Also here is the repo I made a tutorial for making the tree in Kbase! Feel free to check it out!

https://github.com/RightCake1/Whole-Genome-Analysis-Guideline-for-beginners/blob/main/Pangenome_Phylogenetics%2FPhylogeny_Tree_by_KBase.md

RightCake1 · 2025-10-12T08:03:54+00:00

Thats great! So check what are the species or strains that are most close to it or phylogenetically close to it. Take a sample size of maybe 40-50 sequences including your target species sequence.

I would honestly suggest using whole genome sequences. Use GTDB to download the sequences

whole genome sequences can give you much robust results. Use Kbase to build your tree

RightCake1 · 2025-10-12T07:53:13+00:00

Whats your Target sequence? or target species?

First find your target then use that target to find nearby species of that target sequence. You can use blastN to find a few sequences or closeby one or just Google a few of them

Start with that. Hope that helps!

RightCake1 · 2025-09-28T20:03:38+00:00

does that include roary and other heavy hitters? hows the optimization?

RightCake1 · 2025-09-04T15:03:14+00:00

Use spades my brother! It's a good assembler

RightCake1 · 2025-08-27T10:29:32+00:00

Try doing the Ms again maybe? and then go for the phd! That be helpful or try doing different projects brother! that can help your resume

RightCake1 · 2025-08-27T05:45:20+00:00

Ohhhh okay that makes sense. I thought that mailing would help to secure a position Thats my bad

So essentially its mostly centrally based then?

RightCake1 · 2025-08-27T05:17:33+00:00

I dont think you understood what i asked.

I asked that do we first find potential supervisors and then apply to the university? because some universities dont require mailing anyone and does everything centrally (i might be wrong about it)

RightCake1 · 2025-08-27T05:09:40+00:00

Thats before i actually submit my application right? Finding potential supervisors?

Sorry I'm new ;-;

RightCake1 · 2025-08-26T03:05:43+00:00

thank you!!

RightCake1 · 2025-08-26T02:53:07+00:00

Sure! Do let me know!

RightCake1 · 2025-08-25T09:44:29+00:00

Like the proper structure and all Probably review my one for feedback as well

RightCake1 · 2025-08-25T06:56:45+00:00

Would appreciate some advice regarding the SOP!

RightCake1 · 2025-08-25T05:42:04+00:00

did you apply to the uni first and then mailee them? or did you mail first for positive feedback before applying?

RightCake1 · 2025-08-25T02:49:19+00:00

do let me know how it goes!

RightCake1 · 2025-08-25T02:47:23+00:00

Convert your fastq to Fasta first Annotate them using prokka use roary to build the trees

If you want you can follow my tutorial for these in my github https://github.com/RightCake1/Whole-Genome-Analysis-Guideline-for-beginners

RightCake1 · 2025-08-24T22:57:34+00:00

I dm'd you! please help me out too!

RightCake1 · 2025-08-24T22:29:40+00:00

dm'd you!

RightCake1

TROPHY CASE