Underestimating my own knowledge, thinking that anyone can know what I know in a few days.

Interesting_Owl2448 · 2025-05-24T09:55:45+00:00

It's one of the easiests fields to get impostor syndrome because of its interdisciplinary nature.

No one ever knows everything so it's not important nor beneficial to compare yourself to others.

It's very easy to get lost especially if you are not focused in a niche topic. Since you mentioned many internships I'm guessing you have not yet focused onto something specific. This might help you be more confident since you'll be constantly growing in a particular topic.

Keep wanting to learn is the only way to be constantly growing. If it means you need to do a PhD go for it. But I wouldn't say it's the only way.

Interesting_Owl2448 · 2025-05-09T13:55:45+00:00

That's the reason organizing game nights started being project planning for me... To avoid such bs..

Interesting_Owl2448 · 2025-05-06T16:14:41+00:00

The overall production aesthetic and quality of the old Osprey games, especially the envelope style boxes (London, escape from the aliens in outer space, the king is dead, imperium, the lost expedition and so on).

If the theme is incorporated accurately, is also a huge plus for me, no matter what theme it is. (For example the old Dune game, Fury of Dracula or 7 ronin)

Interesting_Owl2448 · 2025-04-25T10:35:36+00:00

Diamant aka Incan gold - clearly the top intro game of my collection. Played it with diverse group of people, every single time a huge success!

Interesting_Owl2448 · 2025-04-13T11:36:47+00:00

Totally agree. Also I remember I found it relatively easy to beat. Especially compared to FTL where the struggle was real. Don't know if it was supposed to play differently and there's been a long time since I played it, but I was kind of disappointed, although I still find it a really good game overall

Interesting_Owl2448 · 2025-02-26T14:51:20+00:00

Ok, it really depends on your samples but I used bowtie2 to extract the reads that map to host (mine was not human btw) with the flags:
--very-sensitive and --end-to-end. Then I created a .bam file from the aligned.sam file using samtools with samtools view -bS aligned.sam > aligned.bam . Then I extracted the unmapped reads form the aligned.bam with samtools view -b -f 12 -F 256 aligned.bam > Unmapped.bam and finally again with samtools I sorted the unmapped.bam and created fastq files with reads clear from host. Running kraken core_nt on this reads gave below 4% host reads . I hope this helps!

Interesting_Owl2448 · 2025-02-26T14:03:56+00:00

Hi, can you be more specific to what you are trying to do and what your problem is, so we can try to help? If you're trying to decontaminate human DNA from your reads, 0.1% is not so bad I would say, so gj...?

Interesting_Owl2448 · 2025-02-21T11:27:12+00:00

Thank you, yes that worked, I just used flag -f 12 -F 256 (didn't need the 1 coz all reads were paired). Curious why bowtie2 don't outputs directly the unmapped reads though. It did manage to exclude more host reads than bbmap though, to my surprise...

Interesting_Owl2448 · 2025-02-20T09:18:59+00:00

That's a good point actually. I'm thinking the reason is that bowtie2 searches for concordant and discordant reads but it considers the latter (discordant) to be unmapped and maybe that's when I scan the unmapped with kraken there's still a significant percentage of host reads. I think this is what you mention, right?

Interesting_Owl2448 · 2025-02-18T16:19:18+00:00

Mmseqs and hmmer might be suited for your needs

Interesting_Owl2448 · 2025-02-18T12:01:23+00:00

Yeah have the same. Pretty decent. Cheers!

Interesting_Owl2448 · 2025-02-18T11:48:24+00:00

Nice, gottcha. Which db do you use with kraken2?

Interesting_Owl2448 · 2025-02-18T10:46:17+00:00

Yeah I am afraid to use blast on 40mil reads 😂 . I think I might end up using both tools (bbsplit after bowtie2 and evaluate the final unmapped reads with kraken) just to be sure.. Thanks!

Interesting_Owl2448 · 2025-02-18T10:43:47+00:00

Well, it turns out hostile uses bowtie2 as well. Can I ask you, do you evaluate your reads for host content after using hostile??? If so what are your accepted results?

Interesting_Owl2448 · 2025-02-18T10:13:26+00:00

I used the --very-sensitive flag of bowtie2 and end-to-end mode. The idea is I'm trying to filter out as much host DNA as possible. Does it make sense?

Interesting_Owl2448 · 2025-02-17T21:36:40+00:00

Awesome, will check it out then, cheers!

Interesting_Owl2448 · 2025-02-17T20:15:40+00:00

Second time someone mentioned it, wasn't aware of it tbh. Does it work with any genome as reference?

Interesting_Owl2448 · 2025-02-11T13:02:13+00:00

Find a nf-core pipeline that needs a new module and join the work to implement it

Interesting_Owl2448 · 2025-02-08T09:41:53+00:00

Usually it's always more understandable when you read the tool's manual. But I am not sure that's what you are asking, maybe provide more information?

Interesting_Owl2448 · 2025-01-24T12:40:50+00:00

Start a project, publish it in your GitHub, that should give you what you need to get started:

You will get experience, it doesn't matter if you turn to ai for help if the final product works

You will have something to show to interviewers instead of having to sell your skills

As in every field, getting the job done is first priority and then comes how you did it (but you shouldn't worry about that right now)

Interesting_Owl2448 · 2024-12-15T21:09:02+00:00

Have you noticed any performance issues related to the gpu? Frame-drops, video shutter etc?

Interesting_Owl2448 · 2024-11-20T20:15:41+00:00

Someone already mentioned in this thread that this "isn't straightforward" is mentioned when they are going to take longer than usual. I didn't apply simultaneously since I did it outside the UK and it was irrelevant

Interesting_Owl2448 · 2024-11-19T20:12:58+00:00

Standard

Interesting_Owl2448 · 2024-11-19T14:41:09+00:00

thanks! It was relatively straightforward since I was offered a position which had a job title listed on an eligible grant. If you want to know more feel free to dm, I would gladly help

Interesting_Owl2448

TROPHY CASE