fastqSampler and writeFastq in shortread package
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@francescadefilippis-7043
Last seen 6.8 years ago
European Union

Hello!

I need to randomly subsample a fastq file. I'm trying to use the shortbread package.

This are the commands I tried:

xx=FastqSampler("~/Desktop/Silano2014_RawReads/1_S1_R1.fastq", 100)

xx
class: FastqSampler 
file: 1_S1_R1.fastq 
status: n=100 current=0 added=0 total=0 buffer=0 
ordered: FALSE 

set.seed(123L);
p1 = yield(xx)

class: ShortReadQ
length: 100 reads; width: 151 cycles

Then I tried to write this new file:

writeFastq(p1,file="subset.fastq", mode="w")

But the file it created doesn't look like a fastq

head subset.fastq

?]K??<????ث?aٲh
Am I doing something wrong?

Thanks

Francesca

 

shortread fastq write • 2.1k views
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Entering edit mode
Mike Smith ★ 5.2k
@mike-smith
Last seen 2 hours ago
EMBL Heidelberg / de.NBI

Hi Francesca,

By default writeFastq() will gz compress the file it creates.  If you want an uncompressed file you have to provide the argument compress=FALSE.  Hopefully this will work for you:

writeFastq(p1,file="subset.fastq", mode="w", compress = FALSE)

Mike

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