Barcode demultiplexing method not to separate multiple sequence runs

[erepolliuchi]

Hi,

I sequenced three runs of the same sample using the Native Barcoding Kit SQK-NBD114-96 (same flow cell, but the sequencing had to be stopped unintentionally, so I ended up with three runs).

It is fine up to the point where the pod5 files in 3 separate folders are basecalled into one bam file. But when I dorado demux them, I get 3 x 96 fastq files (= 3 runs x 96 samples). In my case, since the 3 runs are the same sample, I only need 1 run x 96 fastq files, but the run name appears as a prefix at the beginning of the fastq file, and the file is split.

Is there any way to combine these files so that they are not separated by run by using options in the dorado demux command, etc.?

[HalfPhoton]

Hi @erepolliuchi,
I believe you can simply concatenate each of the fastq file triplets as they're just text.

If these we SAM/BAM files you'd need to sort and merge.

Kind regards,
Rich