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By default, the SRA tools command fastq-dump does not assign /1 or /2 to paired reads. Add --defline-seq '@$ac.$si.$sg/$ri' to fastq-dump command in the get_data.py script.
By default, the SRA tools command
fastq-dump
does not assign/1
or/2
to paired reads. Add--defline-seq '@$ac.$si.$sg/$ri'
tofastq-dump
command in theget_data.py
script.https://standage.github.io/streaming-data-from-the-sra-with-fastq-dump.html
ncbi/sra-tools#56
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