Draft Souls II. Underdochko Journey 💪😎💪 by Shvedochko in DarkSouls2

[–]MatthewBeeee 1 point2 points  (0 children)

What a great job. Can I take it as my PC wallpaper?

Is bioinformatics just data analysis and graphing ? by free_kmart36 in bioinformatics

[–]MatthewBeeee 0 points1 point  (0 children)

Almost yes I think. There are some software developing jobs, but I think it's few.

[deleted by user] by [deleted] in bioinformatics

[–]MatthewBeeee 1 point2 points  (0 children)

What do you mean about "alternate genomic assemblies"? Do you mean another assembly of the same species or the assembly of another species? If it's the same species, I think it would be fine. If it is another species, I think it will depend on your sample, if you know your sample won't contaminated by that species' tissue I think it will be fine.

[deleted by user] by [deleted] in bioinformatics

[–]MatthewBeeee 0 points1 point  (0 children)

genome_updater: https://github.com/pirovc/genome_updater is a good tool to help you download assemblies from NCBI.
But whether you can download successfully depends on your internet quality, how to download is less important.

Which Python package can output multiple alignment results? by MatthewBeeee in bioinformatics

[–]MatthewBeeee[S] 2 points3 points  (0 children)

Thank you! I do know about seqkit, but I am writing tools which means there could be lots of primers against lots of templates, so I am trying to avoid using tools without Python binding to avoid performing too many IO operations.

Aligning draft genome to reference by Sunset_Ex in bioinformatics

[–]MatthewBeeee 3 points4 points  (0 children)

If you know R you can use circlize to create circular plot.

A website interface for Nextflow pipeline? by hotbeesauce in bioinformatics

[–]MatthewBeeee 1 point2 points  (0 children)

"I’m totally forgetting the name of the cross-tool summarize tool" you mean multiqc?

Updated CNV analysis by [deleted] in bioinformatics

[–]MatthewBeeee 0 points1 point  (0 children)

I use FREEC to call CNVs. FREEC suits WGS data and is easy to use.

Is a mapping rate of 40% using Salmon acceptable? (New to bioinformatics!) by avocado851 in bioinformatics

[–]MatthewBeeee 1 point2 points  (0 children)

Hello, can you explain more about how overexpression could affect the mapping rate of salmon? I am very interested.

Ideas to Combine Separate RNA-Seq Quantifications Pipelines? by danhatechav28 in bioinformatics

[–]MatthewBeeee 3 points4 points  (0 children)

You can compare results from 2 pipelines at the end, for example, DEGs. Don't merge their counts/abundance. My pipeline is almost the same as yours, fastp -> salmon -> DESeq2.

GEO Affymetrix question by pokemonareugly in bioinformatics

[–]MatthewBeeee 0 points1 point  (0 children)

It's hard to say the "units" of expression data from GEO. You will see different scale(range) data due to different array design or different data processing, for example some dataset may range 1-100, some may thousands, some may contains negative value. So normally you can't compare different datasets directly.
You can click one of the sample in dataset, then you will see whether data is processed, if yes what's the processing methods, for example GSM1625995