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sheffield-bioinformatics-core / periscope

A tool to quantify sub-genomic RNA (sgRNA) expression in SARS-CoV-2 artic network amplicon nanopore sequencing data.
GNU General Public License v3.0
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Normalisation of amplicon based illumina data #9

Open mattdmem opened 3 years ago

ksw9 commented 3 years ago

Hi, Thank you for a great tool. We're wondering if periscope will perform better when using Nanopore data as compared to Illumina short read data? It looks like periscope can also handle Illumina reads and I'm wondering if short reads will reduce sensitivity of sgRNA. Thank you!

mattdmem commented 3 years ago

Hello,

Thanks for using our tool and sorry for the late reply! The latest version should work with Illumina data, sensitivity depends really. I think for ARTIC network 400bp Illumina data we don't see much difference, for capture data too it seems to work well. Updates to the pre-print coming with these changes and analyses

Matt

ksw9 commented 3 years ago

Dear Matt, That sounds great, thank you for the update! Will look out for the updated preprint. All the best,