Hello,
I submitted two samples for whole plasmid sequencing. I usually get a fasta. fastaq, the histogram and the consensus file. This time they only attached the fastaq and the histogram file. I asked customer service if it was possible that they forgot to attach the rest and they said that there is no missing files and that is all that it generated. According to the histogram, it seems that it worked. I sanger-sequenced the plasmid before I sent and I got a fragment of the sequence without issues, but because I needed a lot of coverage, I sent it for whole plasmid sequence. I have barely used whole plasmid sequence, so I do not know if there was something wrong. The person from customer service could not explain me what happened and they said they would ask the lab.
Receiving only a fastaq file and a histogram file from your whole plasmid sequencing order does not necessarily mean that it has failed. The presence of the fastaq file indicates that sequencing was performed and generated sequence data in the FASTQ format. The histogram file provides information about the quality scores of the sequencing reads. It's possible that the sequencing facility you used does not typically provide additional files such as the consensus file or a separate fasta file. The consensus file is typically generated by aligning and merging the sequencing reads to generate a representative sequence for the plasmid. However, the absence of this file does not necessarily indicate a failure, as the information from the fastaq file can still be used for downstream analysis.
Thank you for your answer @SusantaRoy. They usually attach also the consensus but it wasn't this time. And the customer service person said it may be the template. But danger didn't fail and didn't give me any dirty peaks indicating several sequences present. They said they would run again. But I don't understand why they cannot generate the consensus file with the info from the fastq. I don't have expertise in nanopore sequencing.
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