Question: Is Paired End analysis possible with FASTQC?
6
gravatar for chefarov
3.4 years ago by
chefarov120
Greece
chefarov120 wrote:

Is it possible to pass paired end data on fastqc commandline? The

./fastqc --help

doesn't mention how to do it. It is possible to pass multiple files like

./fastq file1 file2 file3

but it doesn't seem to differentiate somehow SE with PE.

On another post I read that FASTQC is not suited for paired end. However I got confused because inside the Configuration/contaminants.txt file the reads are paired end.

fastqc qc dna-seq paired-end • 11k views
ADD COMMENTlink modified 20 months ago by Stephane Plaisance410 • written 3.4 years ago by chefarov120
2
gravatar for mastal511
3.4 years ago by
mastal5112.0k
mastal5112.0k wrote:

Normally fastqc will analyse the files for the forward and reverse reads separately.

ADD COMMENTlink written 3.4 years ago by mastal5112.0k

Thus, it does not support paired-end data, right? Thanks

ADD REPLYlink written 3.4 years ago by chefarov120
3

Since the two reads of the pair are generated separately, trying to get statistics like per base sequence quality on the combined forward and reverse reads would make no sense. That is not the same as saying that it doesn't support paired-end reads.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by mastal5112.0k
4
gravatar for Ian
3.4 years ago by
Ian5.5k
University of Manchester, UK
Ian5.5k wrote:

We use Fastqc to analyse pre-mapped fastq reads for R1 and R2 separately. For post-mapped paired-end reads you can input the BAM file.

The full list of accepted files from the manual is:

  • FastQ (all quality encoding variants)
  • Casava
  • FastQ files
  • Colorspace FastQ
  • GZip compressed FastQ
  • SAM
  • BAM
  • SAM/BAM Mapped only (normally used for colorspace data)
ADD COMMENTlink written 3.4 years ago by Ian5.5k
3
gravatar for biomaster
3.4 years ago by
biomaster180
San Jose
biomaster180 wrote:

I like to use AfterQC, which can handle pair-end fastq QC

ADD COMMENTlink written 3.4 years ago by biomaster180

Thanks but this doesn't seem to provide decent visualized output

ADD REPLYlink written 3.4 years ago by chefarov120
1
gravatar for Stephane Plaisance
20 months ago by
Leuven area (Belgium)
Stephane Plaisance410 wrote:

After mapping to a reference genome, you can use Qualimap to assess many very instructive facets of your reads

ADD COMMENTlink written 20 months ago by Stephane Plaisance410
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