FASTQ batch downloads from SRA database not working for Windows

reneshbedre / bioinfokit

Bioinformatics data analysis and visualization toolkit

MIT License

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FASTQ batch downloads from SRA database not working for Windows #25

Closed DeevanshuGoyal closed 3 years ago

DeevanshuGoyal commented 3 years ago

Hi,

It seems that the command "bioinfokit.analys.fastq.sra_bd" doesn't work for Windows. The issue seems to be the absence of fasterq function in the Windows version of the SRA toolkit.

Is there any other way to use this function or be able to download large batches of data from the SRA database in a single command?

Regards.

reneshbedre commented 3 years ago

@DeevanshuGoyal ,

bioinfokit.analys.fastq.sra_bd does not work on Windows. You should use it on Mac or Linux OS. You need to have the NCBI SRA toolkit installed and should be in the system path.