Fastq data

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Aaron Hardin

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Apr 10, 2020, 11:06:29 PM4/10/20
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Hi! I’m wondering if the fastqs files are available somewhere? Interested in seeing how many reads come out per barcode and how well the barcode edit distances worked.

Mikolaj Slabicki

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Apr 13, 2020, 9:53:15 AM4/13/20
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Hi Aaron,
NGS sequencing for LAMP-Seq method still needs to be tested with complex barcode combinations on clinical samples. Hopefully, it will happen in the upcoming days.
Best,
Mikolaj

Yaniv Kusuma

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May 17, 2020, 8:45:21 PM5/17/20
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Hello, Any update on this?

I would like to see fastq files as well.

Jonathan Schmid-Burgk

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May 19, 2020, 1:49:55 AM5/19/20
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Hi Yaniv,

Here is a link to example FASTQ data from pooling six barcoded LAMP reactions, of which three were inoculated with RNA:

Positive barcodes: CCCATAAATC, CGACCTAGGA, CACTTAGGAG
Negative barcodes: ATCGGCATCT, GCGATTGTAA, GTTATACGCT

Let me know if you need more infos to the run

Best,
Jonathan

Yaniv Kusuma

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May 19, 2020, 1:58:00 AM5/19/20
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Thanks a lot Jonathan,

If i am right, Did you use C-FIP-Barcode primer for this data?

If yes, what was the reason behind its selection over A-FIP and B-FIP?

Jonathan Schmid-Burgk

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May 19, 2020, 2:05:44 AM5/19/20
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The reason is that the C primer set has higher molecular sensitivity in my hands, please also see the updated Starter Kit protocol.

Yaniv Kusuma

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May 19, 2020, 2:23:41 AM5/19/20
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Hello Jonathan, Any update on experiment result with compressed barcode space? 

kuiku...@gmail.com

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May 26, 2020, 9:14:09 PM5/26/20
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Hi Jonathan, 

I was wondering what was the source of the samples you used to produce that fast file, is that nasal swab, or saliva or something entirely different ?

best, 

David Li

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Jun 11, 2020, 12:13:12 AM6/11/20
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Yaniv: We have yet to try any experiments with the compressed barcode space, but the theory is all there. The focus has been on characterizing/improving the sensitivity as well as validating/optimizing the protocol on patient samples. 

kuikuisven: The FASTQ file on this forum is from RNA spike-ins, but LAMP-seq has been run on clinical samples (oropharyngeal swabs), see the latest updated pre-print. 
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