Fastq data

[Aaron Hardin]

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]

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]

Hello, Any update on this?

I would like to see fastq files as well.

[Jonathan Schmid-Burgk]

Hi Yaniv,

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

FASTQ

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]

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]

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]

Hello Jonathan, Any update on experiment result with compressed barcode space? 

[kuiku...@gmail.com]

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, 

N 

[David Li]

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.