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Issue separating mate pair fastq files from a paired-end sequencing dataset

Hi, I need to analyze RNA-seq reads from the following dataset: https://www.ncbi.nlm.nih.gov/sra/?term=SRP113243

According to the paper and information on SRA site, these are paired-end reads, but when I do fastq-dump --split-files <file>, I only get one fastq file. Also, opening the file, it doesn't look like it is paired-end. I am very confused. Please help!!

next-gen rna-seq rna-seq sequencing fastq
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written by marvel479 • marvel479

Thanks @ATpoint. I will contact the authors about this.

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written by marvel479 • marvel479

1 answer

Your command is correct but there is in fact only one file uploaded, so either the methods are incorrect or the authors did not uploaded the paired files. Nothing you can do about it I fear except contacting the authors.

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written by ATpoint ATpoint

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