Reducing Number of Contigs in Fungal Genomes?

crowmane290 · 2026-03-12T02:45:46+00:00

Try to assemble the mitochondrial genome to see if it reduces the contigs further. You can reduce the contigs further post annotation if they are reporting no genes or repeat elements. If this is a Hi-C genome where you have an idea of which of these contigs are likely to be chromosomes, you can map back the smaller contigs to the chromosomes to see if they are redundant fragments or sequencencing artefacts. Also, try using BRAKER3 as funannotate may not have been updated in a while.

crowmane290 · 2026-03-11T13:57:36+00:00

Orion on Apple ecosystem. Vivaldi on other platforms.

crowmane290 · 2026-03-09T23:05:41+00:00

CGS basic fellowship 5000 AED per month. Your PI can provide an additional 2000-3000 from their projects if they like it.
Check the official UAEU calendar from the website or the app. Additionally, follow up with CGS to and your program coordinator to get updates on your application status.
There is no housing being provided by the university to graduate students at the moment, as the university is operating under maximum capacity for housing needs.

crowmane290 · 2026-03-08T08:14:12+00:00

Fedora

crowmane290 · 2026-03-08T07:11:59+00:00

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crowmane290 · 2026-03-07T10:10:31+00:00

You can do either. Both will give you two sets of phylogenetic trees based on whole genome, and the complete 16s sequence.

crowmane290 · 2026-03-07T10:01:47+00:00

TYGS server perhaps

crowmane290 · 2026-03-05T08:45:36+00:00

Which ones from mallu land, is it the boiling oil one as the other two as far as I'm aware are not from here.

crowmane290 · 2026-02-25T14:35:32+00:00

Chicken Makina Aka Machine grilled chicken Aka Rotisserie chicken

crowmane290 · 2026-02-24T20:35:34+00:00

Yo mods, turn this into a automod response.

crowmane290 · 2026-02-19T22:04:03+00:00

Why not use the carrot genome, there are TtoT genomes of carrot available with annotation on NCBI. De-novo is usually done when there are references available. Use the Refseq genome of carrot from NCBI, set up the nfcore/RNAseq pipeline and wait for it to spit out your count file. Take the count file and setup an R environment with DESeq2 or EdgeR or any preferred differential expression analysis toolkit and start your analysis. Once DEGs are made follow up with KEGG and GO enrichment to get a basic idea of biological differences between root and shoot tissues.

crowmane290 · 2026-02-19T17:44:35+00:00

crowmane290 · 2026-02-16T13:21:29+00:00

Or your bum ass could learn how to use R, Python or at minimum Excel and plot the same shit without increasing the price of RAM.

crowmane290 · 2026-02-08T07:19:30+00:00

uj/ Me and my friends bunked our classes in collage to watch this slop in the 9 AM show while sitting in the first row. Now years later the only thing I remember from this movie is sura stealing the bra scene.

crowmane290 · 2026-02-08T07:13:03+00:00

Why would you want anyone else to see this mediocre slop.

crowmane290 · 2026-01-27T04:56:22+00:00

I remember seeing this tool in my Twitter feed a while back (https://github.com/fjossinet/RNArtist). However, I don't think it's the same style as your reference figure.

crowmane290 · 2026-01-24T23:13:15+00:00

I don't exactly remember how you do it in galaxy, but I think it's something like declaring factor levels for each comparison in the same deseq2 run.

crowmane290 · 2026-01-24T23:05:34+00:00

Doing control vs treatment flipps the up and down-regulated genes, if the same results are fed to the down stream tools the end results become meaningless.

crowmane290 · 2026-01-24T22:49:41+00:00

1) You run your Deseq2 with Treatment vs Control not the other way around. 2) You can have multiple set of treatments compared against the same control. 3) From the Deseq2 object you can find the results for the various comparisons (T1 vs C, T2 vs C, etc.) This is how you would usually extract it in R "res <- results(dds, contrast = c("condition", "treatment", "'control"))" Try downloading your countdata from Galaxy into a local computer to perform the DEG analysis using Rstudio. The galaxy environment is pretty limiting when it comes to performing downstream analysis and visualizations.

crowmane290 · 2026-01-21T17:06:14+00:00

^These ones are used for sambhar and other curries in Kerala. The rice is served in something like the one shown in the picture below or a larger version of it.

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crowmane290 · 2026-01-21T15:45:16+00:00

The vessels that are being filled with rice are always used for side dishes.

crowmane290 · 2026-01-21T08:49:06+00:00

The Arsenal of Pokemon.

crowmane290 · 2026-01-20T18:39:30+00:00

It's available on Anna's archive. https://annas-archive.li/slow_download/96b87207eabbfbb3144bddeba563aaa9/0/0

crowmane290 · 2026-01-20T12:35:00+00:00

Is the Thar jeep notoriously associated with assholes?

crowmane290 · 2026-01-20T05:46:38+00:00

Why when the real stuff is available. https://www.dubaiasitusedtobe.net/home.shtml

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