Some Question About Converting sra format file to fastq format file
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3.6 years ago
Ashley ▴ 90

I have a nanopore sequencing data: https://www.ncbi.nlm.nih.gov/sra/SRX5326468[accn] And I want to convert sra format file to fastq format file. There is an error occured, and help would be greatly appreciate.

Error information: Rejected 1191866 SPOTS because SPOTLEN < 1. Read 1191866 spots for SRR8523633.sra Written 0 spots for SRR8523633.sra

nanopore technology sequencing • 1.3k views
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Difficult to help you without knowing what program and what command failed in this task. See if this works for you. In the far right column on this page there are links to several similar questions that may be useful.

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I think nanopore sequencing data does not have any quality score. Fastq has a quality score. So you can get fast5 file out of SRA check the link how-to-get-nanopore-minion-fast5-from-sra. Later u can use poretools to convert fast5 to fastq.

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Provide the command used, so that we can help you in better way. You can go through 4th post provided in this link. As your data is of oxford nanopore which is SE, you can try using –split-3, where you get all single end reads in separate file.

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3.6 years ago
Ashley ▴ 90

The correct answer is "fastq-dump --table SEQUENCE SRR8523633". And I know the reason.

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What you write here sounds rather disrespectful/arrogant towards the three users trying to provide help. Maybe an issue with the language barrier and you did not intend to sound disrespect, still this is not the way one should interact with other users.

It would also be good if you share why your solution worked given you know the answer, this would help others in the future. YOu can use the edit function to add that to your answer.