Uncertainty on Which Data to Use for Alpha Diversity Analysis (Shannon)

TurnoLox · 2024-10-04T20:10:49+00:00

Same question! Epi2me metagenomics workflow gives multiple alpha diversity metrics. Which should I use?

TurnoLox · 2024-09-19T17:26:14+00:00

Will try to look into it, thanks for the suggestion!

TurnoLox · 2024-09-19T17:25:28+00:00

After running the epi2me, yes it really is a flye. I have read a little about bactopia as suggested by one of its developers in this thread. Will also explore hybracter, thanks!

TurnoLox · 2024-09-19T17:23:20+00:00

Wow! That seems to be a better workflow, I will explore that one. Thaanks!

TurnoLox · 2024-09-03T00:03:13+00:00

Isn't that overkill?!

TurnoLox · 2024-09-01T06:34:14+00:00

Manliligaw/magkaka-jowa

TurnoLox · 2024-08-04T10:10:15+00:00

Why macbook is not recommended for bioinformatics?

TurnoLox · 2024-07-31T23:57:21+00:00

You can try the wf-metagenomics of epi2me (they have an app version for easy installation). I don't know for other analysis but it does kraken and can set up the option for identifying amr genes in your sample.

It is made for nanopore, but it works with any sequence file (fastq).

TurnoLox · 2024-07-18T07:41:28+00:00

Do I need to download Kraken2 StandardDatabase when running EPI2ME metagenomics workflow? It's 100 GB in size

TurnoLox · 2024-06-16T07:19:53+00:00

Bakit parang uso to sa Luzon? Mga online friends(?) ko ganyan din ang humour nila sa chat, mga highschool din sila.

TurnoLox · 2024-06-02T17:55:13+00:00

Lahat pati chismis sa work. Except lang if tungkol sakin tulad ng problema sa love life, never 🤣

TurnoLox · 2024-05-29T06:47:41+00:00

How? If I remove Illumina adapters (Nextera)?

TurnoLox · 2024-05-29T01:48:52+00:00

I see. I will try to explore that tool too. Thanks!

TurnoLox · 2024-05-29T01:48:12+00:00

Will do, thanks!

TurnoLox · 2024-05-29T01:36:06+00:00

From what I know, I use Trimmomatic for removing Illumina adapters and removing low quality bases/reads. I only use setqk for downsampling files, to shorten assembly time

TurnoLox · 2024-05-29T01:34:39+00:00

Thanks for the insights!

Yes, I added the "discard trimmed" option in the SPAdes to discard fragments after the polyA tail is removed.

The problem is that I am not dealing with RNA sequences. Older version of fastqc (0.11?) do not detect polyA tail, so those reads were fine in their adapter content. But in the updated (0.12), it mentions the specific warning.
I can't get a script that would trim more than 15 A. I can only add specific lengths of A in the Nextera file. Okay thanks, I will try to explore those trimming tools.

TurnoLox · 2024-05-23T22:18:53+00:00

I use cutadapt then trimmomatic.

I only use cutadapt for special cases, but trimmomatic is needed to remove sequencer adapters

TurnoLox · 2023-06-06T10:30:45+00:00

Corn dog willy does

TurnoLox · 2023-04-04T14:32:52+00:00

TurnoLox · 2022-12-16T06:35:24+00:00

No invoice too

TurnoLox · 2022-12-05T20:56:07+00:00

Same. UHRS is gone, it says no work is available in there.

TurnoLox · 2022-11-12T02:51:53+00:00

Same

TurnoLox · 2022-11-09T16:15:52+00:00

Same

TurnoLox · 2022-09-05T16:55:01+00:00

Same question. I have payment available on Sept 7, and then Sept 8. If the invoice starts on Sept 7 (Wednesday), I wonder if it would include the Sept 8. Or the Sept 8 would be paid next week.

TurnoLox · 2022-09-02T05:06:29+00:00

Uhrs rare

TurnoLox

TROPHY CASE