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We use fastq_dump to convert the downloaded .sra files to fastq. When the data is single-ended, only one output file is created: Run_XXX.fastq. When the data is pair-ended, the dump usually creates two output files: Run_XXX_1.fastq and Run_XXX_2.fastq, for the paired reads (forward in _1, reverse in _2). Sometimes it creates a third output file, Run_XXX.fastq, where it puts reads that are in the raw data, without their paired read. Normally when this happens, the third file is very small compared to the paired files, and I discard it, but in the current experiment the third file is half the size of each of the paired files. What do you think should I do with a rna-seq run that its fastq dump has a lot of unpaired reads (half the number of the pairs)?
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