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Old 09-03-2015, 03:48 PM   #1
Nicolas_15
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Default Read in mutiple gzipped FastQ files using R

Hi,

I'm stuck in a very basic question of how to upload multiple gzipped files in R on Linux? Could anyone answer it? I'd appreciate your help.

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Old 09-03-2015, 11:56 PM   #2
dpryan
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Just read each one into a different data frame/object.
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Old 09-04-2015, 12:17 PM   #3
Nicolas_15
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thanks, but no easier way to read in? because I have 30 seq libraries in fastq.gz format. It seems gzfile() could achieve the purpose. I'm unsure if I could compress the 30 files and then upload it as a whole. Is anyone willing to commenting this?

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Old 09-04-2015, 01:11 PM   #4
dpryan
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Why do you want to read fastq files into R? There is very very very rarely a good reason to do this.

You can read everything into a single list. At the moment, I'm doing that with ~900 files, in fact. You typically want to use globbing to generate a list of file names and then use something like lapply() to have each one read in and processed in some sort of meaningful way.
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Old 09-04-2015, 01:47 PM   #5
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OK, I see what you meant. Thank you so much!

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