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claraqin / neonMicrobe

Processing NEON soil microbe marker gene sequence data into ASV tables.
GNU Lesser General Public License v3.0
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Read fastq.gz file #4

Closed KaiZhuPhD closed 4 years ago

KaiZhuPhD commented 4 years ago

@lstanish I tried to read fastq.gz file. ShortRead::readFastq() doesn't support direct read from https, which is different from base::read.csv(). A workaround is to download the file to a temp location and read locally. It should work for Windows/Mac/Linux.

https://github.com/claraqin/NEON_soil_microbe_processing/blob/71a59cd195c1983910bf3168ae68a042aa6e5801/code/test.R#L10-L16

claraqin commented 4 years ago

Sorry for the delayed response – it seems like this issue has been resolved because we download to the local file system.