Is Paired End analysis possible with FASTQC?
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.
4 answers
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)
After mapping to a reference genome, you can use Qualimap to assess many very instructive facets of your reads
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