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add --defline-seq to fastq-dump command in get_data.py #18

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johnsolk opened this issue May 2, 2018 · 0 comments
Open

add --defline-seq to fastq-dump command in get_data.py #18

johnsolk opened this issue May 2, 2018 · 0 comments

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@johnsolk
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johnsolk commented May 2, 2018

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.

https://standage.github.io/streaming-data-from-the-sra-with-fastq-dump.html
ncbi/sra-tools#56

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