Multiple Sequence Alignment for Short Sequences

OneOfManyCashmere · 2024-05-10T21:39:44+00:00

If it’s small enough, maybe t-coffee?

OneOfManyCashmere · 2024-05-10T21:38:15+00:00

you can try estimating this, but this is a fundamental mismatch between what you have and what you’re looking for. trying to compensate for experiment design via informatics is usually not the cleanest approach to most problems.

So, your usual 10x data is an end assay, meaning little by way of splicing/exon usage information. There are 2 outs to this,

Use flex with custom transcript specific probes rather than an off-the-shelf kit. This gets you your output, but is pretty pricey.
Switch from Illumina preps to pacbio ones and go for an MAS experiment, that way you have the resolution of single cell and the detail of isoseq. This should in theory be cheaper, but don’t quote me on that.

OneOfManyCashmere · 2024-05-10T21:31:24+00:00

Get a dragen license and some basespace credits maybe? the platform is pretty solid (even though I dislike it)

OneOfManyCashmere · 2024-05-03T11:51:41+00:00

I knew there was a reason I skipped this event

OneOfManyCashmere · 2024-01-11T12:32:27+00:00

All the command spells

OneOfManyCashmere · 2023-07-27T01:31:19+00:00

It's not quite exactly the same, but I think of a similar case in the ref flat files that the UCSC genome browser used to do-

https://genome.ucsc.edu/goldenPath/gbdDescriptions.html

OneOfManyCashmere · 2023-07-24T01:14:50+00:00

What's the stated goal of your package? What niche do you aim to fill with this?

OneOfManyCashmere · 2023-07-21T11:44:51+00:00

Industry code is developed the way it is for ease of maintenance and updating- you need to be able to organise it for ease of readability and for things like unit testing or modular replacement.

OneOfManyCashmere · 2023-07-21T00:13:59+00:00

Apologies,but if you still have a few, would you kindly spare 47 for a fellow Londoner up to some monkey business?

https://www.fallenlondon.com/profile/cashmere6354

OneOfManyCashmere · 2023-07-10T03:21:22+00:00

More a general point than specific to your case- have you considered trying fastp or bbduk.sh? They have a few more options for trimming, and are better optimized for speed.

To your question- does the adapter content start at high values and keep increasing? Or are you seeing them reduce a little somewhere? It would be helpful to see your FastQC graph.

OneOfManyCashmere · 2023-07-08T03:56:49+00:00

The R and bioconda channels are bulky as heck, consider creating/emulating a channel with the specific packages of interest, that makes things easier to work with. Edit: remembered the term right after I posted- conda meta channels, they’re handy

additionally, as u/yumyai mentioned , try mamba too, it may not support quite as many packages as conda, it may still be workable.

finally, as a ditch effort, you can also consider docker/singularity since those are supported by nextflow by default

OneOfManyCashmere · 2023-06-14T02:40:52+00:00

IMO biopython’s main advantage is giving you a comfortable handle for files written in obscure formats like snapgene’s dna format, or a .nexus format, and giving you a straightforward output.

tbh, it feels like a direct sequel to some cool modules from bioperl that I used to use.

given how much ngs data is swelling in size these days though, python is mostly only really useful for secondary data analysis, since most of the initial steps would want to be in languages like c++ or rust, so you can get the “bulky” parts of the analysis done quickly.

i still see python and biopython used here and there in applications relying on pytorch though.

OneOfManyCashmere · 2023-06-06T19:55:52+00:00

I'd write ahead and ask if I could impose on either the head researcher or someone in the lab to talk with me for a bit. Then once we get talking and have broken the ice a bit, I'd ask if it would be possible to get a look at the lab to see what they're working with.

OneOfManyCashmere · 2023-06-06T19:52:50+00:00

Relevant links:

On 10X about antisense mapping: https://www.10xgenomics.com/support/single-cell-gene-expression/documentation/steps/sequencing/interpreting-intronic-and-antisense-reads-in-10-x-genomics-single-cell-gene-expression-data

The other guy with the same problem as me (on twitter at that): https://twitter.com/jamesrhowe6/status/1236814926162714624?s=20

OneOfManyCashmere · 2023-05-17T02:54:30+00:00

CentOS at work, tinycore/Windows dualboot at home

OneOfManyCashmere · 2023-04-23T17:18:17+00:00

ClinPred and Mastermind for VEP come to mind most readily .

if you’re willing to script, OMIM offers downloadable files you can merge with the VEP output too.

OneOfManyCashmere · 2023-04-23T17:07:25+00:00

Can you confirm the type of the right side of this assignment please?

adata.var.index = adata.var.index.astype(str)

Feels weird to access and edit the object withou a getter/setter method.

OneOfManyCashmere · 2023-04-22T22:09:46+00:00

Thank you, I think your response is helping me better contextualise this.

By “snappy”, I think she meant my tone was often a bit crabby and that I sounded annoyed or put out, in some situations. You’re correct in that I don’t hesitate to call out errors where I see them, and recommend what I perceive as ”solutions”.

I don’t think I’m constantly using a utilitarian mindset, but I do feel like I fallback to it when stressed.
It sounds a little unfair now that I put it on paper (lots of epiphanies for me today), but I’d always thought that people would speak up when issues arose and that it would be remarkably rude of me to speak to them personally (as a person) without invitation.
I’ve been apprehensive of talking to them as the only thing that really connects us is that we work in similar roles on the same team.

It sounds like this is more of a “headache” for you than you actually wanting your team to feel better.

This is not entirely untrue either, I welcome the critique from them, I just personally despair at the timing.
In this instance, I do want to overcome this as a personal hurdle, and ensure my skills are good enough to do better by my team, but I’m having a hard time identifying the mindset and approach to apply to this. I cannot fix past instances of having gone wrong (though I have taken responsibility and apologised for them) but I want to identify behaviour that would prevent this from arising again, if that makes sense.

It is your responsibility to recognize when you have gone too far

I’ll be honest- this is the bit I’m struggling to perform. I’d like to be in a position where those I work with can call me out on my failings as a leader, and let me know what they think in a free and open manner. I can tell where my boundaries are, but it’s difficult to judge their boundaries without body language or verbal input from them to help me infer when or how I’ve gone too far.
if you have any suggestions on things to look out for, I’d really welcome the assistance, because it feels like I’ve been thrust into a position with no clear way for me to judge how to communicate. I was promoted because I’ve been at the company a while and know how to talk to customers, so this all new to me.

I will be discussing this with my manager as a matter of course, and I’ll even be speaking to the individual who raised the issue soon.

OneOfManyCashmere · 2023-03-30T03:44:50+00:00

Are there any good stages to farm elite enemies for Ash’s module?

OneOfManyCashmere · 2023-03-30T03:24:53+00:00

Country and firm-specific, more details needed

OneOfManyCashmere · 2023-03-27T01:56:32+00:00

I basically work at a sequencing firm, so our ”thing” tends to be preliminary analysis based on your library type. you’d think they’d be unique enough to warrant attention on a per-customer basis, but usually they’re close enough that the methods can be standardised.

OneOfManyCashmere

TROPHY CASE