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fastq file to sample mapping for MinION data

I have received 2448 separate fastq files generated by sequencing 48 samples on a MinION. How do I know which files belong to the individual samples?

fastq
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updated by seidel seidel • written by kiapriscilla • kiapriscilla

1 answer

You will have to ask the entity/person that sequenced this data. Were these samples barcoded? Way ONT creates output files there will likely be more than one for each sample.

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written by GenoMax GenoMax

Thank you so much GenoMax, Yes all the the samples were barcoded

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written by kiapriscilla • kiapriscilla

Were they demultiplexed? If they were then there should be folders with names like "barcode01" "barcode02" in the default "fastq_pass" folder. You will need to get the metadata of which barcode corresponds to which sample from your sequence provider.

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written by GenoMax GenoMax

I received 4 sperate folders one-fast5 pass-containing 2428 files, and fast5-fail; fastq-pass containing 2428 files(with the same IDs like the Fast5 files (eg FAQ44519-pass-44eef5d2-0.fastq; -FAQ44519-pass-44eef5d2-1.fastq;---til 2428.fastq.

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written by kiapriscilla • kiapriscilla

Looks like the samples are not demultiplexed. You will need to know what barcode was used for what sample to do the demultiplexing. It may be simpler/easier for your sequence provider to demultiplex the data.

You have some options here: Demultiplexing MinION reads

If you are an experimental scientist then this may be a bit daunting task. See if you can ask sequence provider if they will demultiplex the data for you.

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written by GenoMax GenoMax

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