Is Paired End analysis possible with FASTQC?

Question

[chefarov]

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.

Answer 1

[mastal511]

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

[chefarov]

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

[mastal511]

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.

Answer 2

[Ian]

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)

Answer 3

[biomaster]

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

[chefarov]

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

Answer 4

[Stephane Plaisance]

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