Rqc for RNA-Seq data
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@kritikamish99-9648
Last seen 5.6 years ago
India

Hello members,

I am new in rnaseq analysis. I am running Rqc for my files. can any one explain me what is "extdata/E-MTAB-1147" and how to locate my file by giving path command. I am usnig linux machine for path argument how to locate the directory.

Thank You

Rqc • 2.5k views
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@steve-lianoglou-2771
Last seen 12 months ago
United States

You are presumably talking about this line in the Rqc vignette:

folder <- system.file(package="ShortRead", "extdata/E-MTAB-1147")

The system.file function loads a file that can be found in the specified path from the root of the package that is specified. This allows for a mechanism for R to access files that are provided by a package which abstracts away the actual location that the system is configured to install R packages to. See the help page in ?system.file for more information. If you go to the directory that the ShortRead package is installed in your system, you will find an extdata folder, and you can take it from there ...

To answer your question about what that file is, it says so right in the Rqc vignette:

The next step is to determine the location of the FASTQ files that should be analyzed. The example below, uses sample files provided by the ShortRead package, but the user must modify this location accordingly, in order to reflect the actual location of the files that need QA.

So, they are sample (small) FASTQ files that are distributed with the ShortRead package for the purposes of running example code (and, likely, unit tests)

 

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@wdesouza
Last seen 3.3 years ago
Brazil

The rqc function uses list.files function to search a pattern inside a folder defined by the path. You can run list.files first with the same parameters to see which files the rqc funtion will process. An exemple (using your path):

folder <- "/home/Downloads/Work_Kriti/NGS_Data"
list.files(path = folder, pattern = ".fastq.gz")

Printed files are the files that you want the Rqc to process? If yes, just replace the function. An example:

folder <- "/home/Downloads/Work_Kriti/NGS_Data"
rqc(path = folder, pattern = ".fastq.gz")

In this case, you don't need to use system.file function. The examples in Rqc's vignette use this function to get folder path located inside ShortRead package (as mentioned by Steve Lianoglou).

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Thanks Welliton Souza ..

This was really help full. And i got output also.

Thanks ..

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@wdesouza
Last seen 3.3 years ago
Brazil

Rqc automatically process multiple files in parallel. The multicoreWorkers function returns the number of available processing units.

The rqc function generates only one report file for all FASTQ files. The output directory of report file is defined by outdir parameter and the name of the report file is defined by file parameter.

If you want to have more control on report file, such as generating more than one report, use rqcQA and rqcReport functions instead of rqc function. An exemple using your code:

folder <- "/home/Downloads/Work_Kriti/NGS_Data"
files <- list.files(path = folder, pattern = ".fastq.gz")
# process all FASTQ files and store result data
result <- rqcQA(files)
# generate report for the first 10 FASTQ files
rqcReport(result[1:10])

As mentioned by Steve Lianoglou, please read the manual of the ?rqc?rqcQA and ?rqcReport functions.

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@kritikamish99-9648
Last seen 5.6 years ago
India

Thanks Steve Lianoglou for help. 

Also i need help  in this line  "rqc(path = folder, pattern = ".fastq.gz")". I understood the path is the location of my file.  But my question is  , in linux to go to specific directory we write /directory/filename but in R (path= )  how i will specifying   "path =  " 

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I am getting such error:-

Error in rqcQA(files, sample, n, groupFactor, BPPARAM = BPPARAM) : 
  Input files were not provided.
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You're going to need to provide the code that you have run which leads to the error so that we can have a reproducible example to work with. Secondly you will also need to provide output from sessionInfo()

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This is the code i am running

> folder <- system.file(package="ShortRead", "home/Downloads/Work_Kriti/NGS_Data")
> rqc(path = folder , pattern = "File1_R1.fastq.gz")
Error in rqcQA(files, sample, n, groupFactor, BPPARAM = BPPARAM) :
  Input files were not provided
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@kritikamish99-9648
Last seen 5.6 years ago
India

Hello member In Rqc how to define output file name for each sample. I am using code

rqc(path=folder , pattern = ".fastq", openBrowser = FALSE, outdir = "/home/Downloads/Work_Kriti/NGS_Data/" , file="Rqc_file")

I have 66 paired samples so if i give pattern as .fastq it will run the quality check per sample. But what will the file for each sample. Thank You.

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And what is the fucntion of

workers = multicoreWorkers()

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Please read the help page for the multicoreWorkers function. You can do that by typing ?multicoreWorkers into the R console. That function is part of the BiocParallel library.

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ok. I need help for my first question.

In Rqc how to define output file name for each sample. I am using code 

rqc(path=folder , pattern = ".fastq", openBrowser = FALSE, outdir = "/
/home/Downloads/Work_Kriti/NGS_Data/" ,  file="Rqc_file")

I have 66 paired samples so if i give pattern as .fastq it will run the quality check per sample. But what will the file for each sample. 

Thank You.

 

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@kritikamish99-9648
Last seen 5.6 years ago
India

ok

Thanks for the help Welliton Souza !!!!!!!! 

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