Hi all,
I recently did a nanopore run using the ligation sequencing kit with native barcoding. I had a high amount of reads and data generated.
The biggest issue I have is that when I demultiplexed, there are a high amount of unclassified fastq file.
I was wondering if anybody has experience with this? or what I could do to resolve this?
@Christian I actually did find a solution. It involved using blast and python to match the reads up. It wasn't great though
It the problem which can't be solved with any other tool. The problem arises due to errors in sequencing (library prep etc.) and base calling. And since the base called data could not find correct barcode sequences, it can't be binned in specific barcode and thus end up in unclassified. The only thing which can be done is use the newer version of base caller (guppy) or any other base caller.
Article Deepbinner: Demultiplexing barcoded Oxford Nanopore reads wi...
I am a bit sceptic how you use blast etc to classify the data into barcode bins. There were no information of the barcode that was the reason that reads ended up in unclassified group. With no barcode information, how can a homology search tool be used?
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