barcoding | Naïve barcode deconvolution for amplicons | Barcode Processing library

by nanoporetech Perl Version: 1.0.0 License: MPL-2.0

X-Ray Key Features Code Snippets Community Discussions(3)Vulnerabilities Install Support

kandi X-RAY | barcoding Summary

barcoding is a Perl library typically used in Utilities, Barcode Processing applications. barcoding has no bugs, it has no vulnerabilities, it has a Weak Copyleft License and it has low support. You can download it from GitHub.

This repository is part of the ONT Barcoding Protocol for amplicons.

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Quality

Security

License

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Support

barcoding has a low active ecosystem.

It has 6 star(s) with 1 fork(s). There are 44 watchers for this library.

It had no major release in the last 12 months.

There are 0 open issues and 2 have been closed. On average issues are closed in 296 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of barcoding is 1.0.0

Quality

barcoding has no bugs reported.

Security

barcoding has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

barcoding is licensed under the MPL-2.0 License. This license is Weak Copyleft.

Weak Copyleft licenses have some restrictions, but you can use them in commercial projects.

Reuse

barcoding releases are available to install and integrate.

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barcoding Key Features

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barcoding Examples and Code Snippets

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Community Discussions

Trending Discussions on barcoding

Convert data.frame to Binary Matrix

How to demultiplex BCL data with two different barcoding systems?

Accuracy of barcodes

QUESTION

Convert data.frame to Binary Matrix

Asked 2021-Jan-11 at 02:37

I'm using the CATALYST package to analyze CYTOF data.

One of the commands requires a table in the format of a binary matrix.

I made the table in a .csv document and read it into R, which returned a dataframe-

...

ANSWER

Answered 2021-Jan-11 at 02:19

Starting with a frame:

Source https://stackoverflow.com/questions/65660394

QUESTION

How to demultiplex BCL data with two different barcoding systems?

Asked 2020-Sep-14 at 09:47

I was wondering if anyone has experience in demultiplexing BCL files from Illumina with two different barcoding systems in one go?

we would like to know whether it is possible to use different, barcoded Tn5 adaptors during tagmentation and then use those Barcodes in combination with the barcodes on the sequencing primers to demultiplex the samples.

Has anyone has experience with this kind of analysis? Is it possible to only add the Tn5 sequence to the primer sequence before demultiplexing and use it in the BCL2fastq run?

thanks

Assa

...

ANSWER

Answered 2020-Sep-14 at 09:47

I'm not very well aware of Tn5 adaptors library but I will give it a shot.
In theory, it should be possible. bcl2fastq can demultiplex anything as long as you give it a proper samplesheet and a correct --use-bases-mask argument.

If you need to demultiplex all samples with a combination of two barcode system, you will have to create a samplesheet with a line for each combination that can be found. You also need to know at which cycles the Tn5 adaptors are sequenced.

For example lets say my original samplesheet is like:

Source https://stackoverflow.com/questions/63879811

QUESTION

Accuracy of barcodes

Asked 2020-Jun-20 at 19:25

In books (e.g. "Barcodes for Mobile Devices", ISBN 978-0-521-88839-4), Papers (e.g. "Bar Codes May Have Poorer Error Rates Than Commonly Believed", DOI: 10.1373/clinchem.2010.153288) or websites information about the accuracy or error rates of barcodes are given.

The given numbers vary for e.g. Code39 from 1 error in 1.7 million, over 1 error in 3 million to 1 error in 4.5 million.

Where do these numbers come from and how can one calculate it (e.g. for Code39)?

In the definition of Code39 in ISO/IEC 16388:2007 I also couldn't find usefull information.

...

ANSWER

Answered 2020-Jun-20 at 19:10

Got to barcodefaq site you linked to and click on the Barcode type e.g. UPC and you will get a PDF that explains the methodology used. The article cited explains the error encountered as well as containing links to further informatiion.

Source https://stackoverflow.com/questions/62490377

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install barcoding

You can download it from GitHub.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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