Using readFastq in R

[Hparker]

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

[Wolfgang Huber]

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

[blakeoft]

Are you sure that the fastq files are in that directory?

[Hparker]

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

[SylvainL]

Try to import one file only...