We had same set of sample ran on nanopore platform twice.

The issue on hand is.

First run was done it was nearly done but the power went off. Second run was done completely with enough sequencing depth.

Now the question I ran the analysis with the second set which was complete that set of result I have. But so far I have't ran the first part.

Question1 : if I run the first part do i get major differences? in the result

Question2 : would it be advisable to merge both run since they are now can be called as twi different batches plus would be bring drastic changes in the output ? And in terms of tool for merging I googled which shows poretools.


1 Answer 1


It is entirely unclear which type of analysis you aim to do. You probably should be more specific when asking questions.

That said, given that the run was going perfectly fine until a power issue stopped it, all data produced should be fine and you can indeed combine those runs.

You probably shouldn't bother with poretools. If you are using fastq files to start your analysis you can just cat the basecalled files together. Also after alignment, you can merge the bam files. If your analysis requires the fast5 files then you can probably just put these in the same folder, but you should tell us which analysis you are doing.

  • $\begingroup$ So we have gut mircobiome sample ..between two groups. For classification Im using kraken2 and the output is used for downstream analysis using phyloseq $\endgroup$
    – kcm
    Feb 20, 2021 at 7:55

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