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Old 10-17-2014, 08:23 AM   #1
buthercup_ch
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Location: Japan

Join Date: Apr 2014
Posts: 40
Default Starting with Bioconductor. How to import .fastq files?

Hi everyone.

Hope you can help me. I'm totally beginner in this Bioinformatics world, trying to understand (and analyze if possible) data from RNA-Seq experiment. The final goal is to asses differential expression.

To start, I wanted to import my raw sequences (.fastq) into R Bioconductor, following the sample workflow described on the website:

dataDir <- <...>
fastqDir <- file.path(dataDir, "fastq")
bamDir <- file.path(dataDir, "bam")
outputDir <- file.path(dataDir, "output")

where <…> indicates information provided by the user.

And here is where I get completely lost… Can anyone explain me what is the information I'm supposed to introduce??

Thank you in advance!!
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Old 10-17-2014, 08:45 AM   #2
dpryan
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Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

Honestly, using R for the initial steps is just more trouble than it's worth (you'll need it to do the differential expression though!).

It's likely that those lines are just setting up variables so subsequent steps know where to find different types of files. So, you have a single base directory, held in the "dataDir" variable, with fastq, bam, and other files held (and likely produced) in subdirectories.

So, if your use directory were /home/buttercup_ch, then:
Code:
dataDir <- "/home/buttercup_ch"
fastqDir <-file.path(dataDir, "fastq")
bamDir <- file.path(dataDir, "bam")
outputDir <- file.path(dataDir, "output")
Would do the following:
Code:
> fastqDir
[1] "/home/buttercup_ch/fastq"
> bamDir
[1] "/home/buttercup_ch/bam"
> outputDir
[1] "/home/buttercup_ch/output"
I assume that you would then need to copy your fastq files into the place specified by "fastqDir".
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Old 10-17-2014, 08:10 PM   #3
buthercup_ch
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Location: Japan

Join Date: Apr 2014
Posts: 40
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Hi dpryan!!

This is the line I was using…
dataDir <- (Users/Buthercup_ch/酢:Su/ 酢:Su-Projects/RNA-seq/
RAW sequences/FastQC Reports/St4_DE/St4_DE_t1_ACAGTG_L007_R1_001_fastqc)

I knew it must be some beginner stupid mistake. I have never really use R, more than to built a box plot. I'm nowadays going deeper into it.

Thank you very much!!! :-)

Last edited by buthercup_ch; 10-28-2014 at 07:58 PM.
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