Question: Fastqc And Require Tools
5
gravatar for Ric
5.8 years ago by
Ric160
Australia
Ric160 wrote:

Hello,

FastQC ( http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ ) provide an overview what is wrong with a Fastq file.

However, it does not provide any tools to fix the problems. What kind of tools have to be used to fix the problems?

Thank you in advance.

ADD COMMENTlink modified 4.0 years ago by Phil S.630 • written 5.8 years ago by Ric160
9
gravatar for Jorge Amigo
5.8 years ago by
Jorge Amigo10.0k
Santiago de Compostela, Spain
Jorge Amigo10.0k wrote:

FastQC is just an informative tool, very useful in my opinion to evaluate how the lab sequencing jobs have performed before going into mapping. but as any informative tool, it just tells you what's going on down there, and of course you are the one ultimately having to curate those reads in case you need to. but you'll have to know that there are things that may be curated, and there are others that you won't be able to do anything with them.

since the available tests performed by FastQC are multiple, there isn't a particular to fix the reported errors if any. things like the "per base sequence quality" for instance may be solved by simple sequence trimming if the reported error is that the last 3 bases are always wrong, so they should always be removed from posterior analysis. other error reports may be also solvable by simple scripting, but most of them, such as "per sequence GC contect", are purely descriptive, and in case they fail to pass the FastQC thresholds there's nothing you can do about them but to repeat the lab sequencing if wanted.

ADD COMMENTlink written 5.8 years ago by Jorge Amigo10.0k
4
gravatar for Neilfws
5.8 years ago by
Neilfws47k
Sydney, Australia
Neilfws47k wrote:

The FASTX toolkit may help in some cases; there are tools to filter, trim and clip low-quality sequence. There are also some tools around to "heal" sequencing reads, which may be able to correct platform-dependent systematic errors.

However, as Jorge says, QC generally tells you whether or not something quite fundamental is wrong at the experimental level. If it is, you can't always just "fix" it computationally.

ADD COMMENTlink written 5.8 years ago by Neilfws47k

+1 here. I guess I focused too much in how I think FastQC results should be taken into account, rather than in answering the question itself. yes, FASTX toolkit would be the approach I too would recommend for anyone willing to play around with fastq file, plus its integration in Galaxy may reduce the slope of its learning curve.

ADD REPLYlink written 5.8 years ago by Jorge Amigo10.0k
2
gravatar for optimuscoprime
4.0 years ago by
optimuscoprime140 wrote:

You could try https://github.com/optimuscoprime/autoadapt

It will remove contaminant adaptors and primers, as identified by FastQC, as well as removing low quality sequences

ADD COMMENTlink written 4.0 years ago by optimuscoprime140

it would be nice if you could give some support on using autoadapt on issues raised in github and also via email. Thank you

ADD REPLYlink written 2.6 years ago by eva10
1
gravatar for Phil S.
4.0 years ago by
Phil S.630
Stuttgart, Germany
Phil S.630 wrote:

For Illumina Sequencing i would suggest Trimmomatic, it is kind of designed for illumina and has more specific options. However, fastX is very useful!

ADD COMMENTlink written 4.0 years ago by Phil S.630
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