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Old 12-16-2014, 04:22 AM   #1
Hparker
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Default Using readFastq in R

I have converted some downloaded SRA files from GEO and have converted these to Fastq files but now I am trying to import the data into R and having trouble with this: I get an error message:

readFastq("/Users/parker/Desktop/Bioinformatics/sratoolkit.2.4.2-mac64/bin")

Error: Input/Output
file(s):


Please could you let me know what I might be doing wrong and what I can do to solve this problem.

Many thanks
Hannah
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Old 12-17-2014, 11:13 AM   #2
Wolfgang Huber
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Dear Hannah
Have a look at this posting guide: http://www.bioconductor.org/help/support/posting-guide for suggestions how to ask questions in a way that permit others to give a useful answer (esp. the 'Key points").
Kind regards
Wolfgang
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Old 12-17-2014, 11:22 AM   #3
blakeoft
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Are you sure that the fastq files are in that directory?
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Old 12-18-2014, 12:42 AM   #4
Hparker
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I located the SRA files in the folder 'bin' within the sratoolkit.2.4.2-mac64 folder, so that the SRA files and the fastq-dump are within the same folder. Using the terminal, I then converted the SRA files using ./fastq-dump -A SRR836215 SRR836215.sra for each files separately. The fastq files were then loaded into the same folder, underneath each SRA file.

I then downloaded the ShortRead package from bioconductor into R and used library(ShortRead) and then readFastq("/Users/parker/Desktop/Bioinformatics/sratoolkit.2.4.2-mac64/bin")

This took some time and then I got the error message:

Error: Input/Output
files:

.... and a list of all the files

Hope this is more helpful
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Old 12-18-2014, 04:59 AM   #5
SylvainL
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Try to import one file only...
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