Pipeline QC metrics

[royfrancis]

The pipeline doesn't seem to generate any report so I was wondering if it is possible to get/create QC metrics for read quality (FastQC) and alignment qc. I am interested to know if reads are of good quality and how many are mapping and where in the genome as well as duplication rate etc. If I were to manually run a post alignment qc using RseQC, qualimap, QoRTs etc, which bam file would I use?

sample.filtered.Aligned.GeneTagged.UBcorrected.sorted.bam 
sample.filtered.tagged.Aligned.toTranscriptome.out.bam
sample.filtered.tagged.Aligned.out.bam
sample.filtered.tagged.unmapped.bam

[cziegenhain]

There is a folder with some stats and a few plots concerning where reads map. zUMIs_output/stats

For further QC-ing, sample.filtered.Aligned.GeneTagged.UBcorrected.sorted.bam is the final file to use!

[royfrancis]

That was helpful. Thanks!