FastQC in a pipeline

[graceqy]

Hi,

We are running fastqc with the fq files before alignment with STAR. For now the fastqc output is a html file. I was wondering:

1. Could any of the output from fastqc be used to feed STAR for trimming purpose, pls?

2. How do you process and evaluate PE reads, pls?

3. For now the fastqc output is a html file. If we want to feed STAR with certain fastqc output parameters, is there a way to generate a QC report that we could extract information from for STAR?

Thanks,
Grace

[GenoMax]

FastQC only QC's data. It does not have any functionality for post-processing data (e.g. trimming). You will want to use a dedicated trimming program for that (examples are BBDuk.sh, trimmomatic, cutadapt, skewer etc).

In general if your libraries are good (i.e. no gross adapter dimer contamination etc) no trimming should be required. Most aligners (STAR should too) will soft clip reads during alignment.

FastQC also generates a zip file that has multiple text files (which are used for generating some of the graphics). Take a look at those for getting at the QC data.