How to evaluate the performance of a transcript assembly?

13 September 2012 0 10K Report

I'm learning to use Trinity for transcript assembly. How do I evaluate the result? I can only think of N50, number of transcripts, and mapped reads. What else can I calculated?

Badges
Science topic

More Kai Wang's questions See All

Why does the MFDFA algorithm need to calculate the profile of the time series?

As described in the Multifractal detrended fluctuation analysis (MFDFA) algorithm, it at first calculates the profile of the time series, and then other steps are operated on the profile....

05 August 2024 9,366 2 View

Differences between deep seated landslides and slope destabilization?

Hi, Could someone explain the primary differences between deep-seated landslides and slope destabilization? In particular, definition and characteristics, mechanisms and triggering factors,...

02 August 2024 4,212 2 View

A question about arbuscular mycorrhizal???

How long it takes for arbuscular mycorrhiza to establish and produce benefits under experimental conditions？

25 July 2024 5,208 2 View

Is it possible to run the AIMD within a system using virtual crystal approximation (VCA)?

I want to study the thermal properties of a mixed system which is constructed by virtual crystal approximation in VASP. When I try to run the ab initio Molecular Dynamics of this system in VASP, I...

19 July 2024 6,569 3 View

If I want to invent my own hypothesis testing method, where should I get started ?

15 July 2024 5,376 5 View

Recommendations for Rapid Publication Journals in Traffic and Transportation?

I am currently working on a research paper focused on the control of Connected and Autonomous Vehicles (CAVs) utilizing multi-agent reinforcement learning methods. At this stage, I am seeking a...

14 July 2024 2,620 2 View

I've earned 1 best paper award and 4 best oral presentation awards. What should I do next?

I've earned 1 best paper award and 4 best oral presentation awards. What should I do next to elevate my academic capabilities to the next level ?

14 July 2024 6,071 5 View

How to start writing an anti-virus software ?

I read several information security books. How do I start writing anti-virus softwares ？

13 July 2024 8,180 1 View

Are my cells contaminated with mycoplasma?

I suspect my cells are contaminated with mycoplasma. I fixed the cells with 4% PFA and stained them with DAPI. Below is the image I obtained. I don't observe the typical small, rounded DAPI foci...

11 July 2024 7,786 3 View

How to distinguish the DRX prior austenite grains (PAG) by EBSD of the martensite transformed from PAG （Ausforming）?

During the heavy warm rolling process, austenite undergoes dynamic recrystallization (either DDRX or CDRX), and then transforms into martensite upon quenching. Is there a way to distinguish from...

11 July 2024 7,602 1 View

The Optimal Experimental Approach for Gene Function Analysis?

What is the most suitable experimental setting to understand the consequences of a particular gene: (1) targeted degradation of the specific transcription factor (TF) of the gene, followed by...

04 August 2024 6,265 1 View

How is the bacterial genome's high protein count verified as genuine despite 800+ contigs and good metrics (98.55%completeness, 0.68% contamination)?

Given that the bacterial genome has over 800 contigs, but its quality metrics are good, with a completeness of 98.55% and a contamination of 0.68% as assessed by CheckM, what specific validation...

01 August 2024 1,514 1 View

How to we see transcription activity of the bhlh79 family is at the N-terminal or C-terminal?

I'm a PhD Student. From Northwest Agriculture and Forestry University China. My Problem is this I start my work on bhlh79 transcription factor gene. I do my Y2H 5 time but the colonies appear on...

30 July 2024 1,412 8 View

What happens in snapTotal- seq?

What happens in snapTotal- seq? (Single-cell Total-RNA Profiling Unveils Regulatory Hubs of Transcription Factors https://www.nature.com/articles/s41467-024-50291-3) In this protocol, several RT...

18 July 2024 10,010 0 View

Is it possible to generate a (semi-)permanent "transcription bubble" within a replicable plasmid?

I was wondering if it is possible to form a permanent open "ssDNA bubble" similar to a transcription bubble (>13 nucleotides) within E. coli. These criteria are important: 1. Open ssDNA...

07 July 2024 8,275 5 View

Cloning 1334 bp insert into 6.1kb vector using HiFi DNA assembly/Gibson assebmly cloning ?

Hello, I am trying to clone 1334 bp insert into 6.1 kb vector using HiFi DNA assmebly/Gibson assembly kit. I am taking 100ng of vector and 1:5 molar ratio of vector: insert and 4 hrs of...

27 June 2024 9,652 2 View

Is DNase I (RNase-Free) necessary to be used before cDNA synthesis?

I want to isolate RNA from bacillus subtilis using the QuickRNA Fungal Bacterial Miniprep Kit from Zymo Research and further reverse transcriptase to cDNA using the ReverTra Ace qPCR RT Master Mix...

27 June 2024 2,951 5 View

Can you publish your dissertation after the data has been destroyed?

Hello, Can I publish my dissertation even though the original data has been destroyed in line with my university's ethical procedure? Data was to be destroyed upon completion of my degree. I'd...

25 June 2024 9,580 0 View

To do gibson assembly cloning can I use DH5alpha strain of E. coli. for transformation?

20 June 2024 774 1 View

Why I am not getting colony after transformation in Dh5alpha?

I am trying to do gibson assembly cloning. I have two fragments for gibson assembly cloning (plasmid backbone and insert). After gibson assembly reaction I have transformed this in E. coli....

19 June 2024 6,404 4 View