RNA-Seq and ATAC-Seq quality check

Question

[qudrat.nii]

Hello

I have bam files for RNA-Seq and ATAC-Seq and I want to see the quality of these files before I do any analysis. Please tell me what stuff should I look into and which tools are required.

Thank you

[bk11]

I would start with fastqc to check the quality of reads and any adapters present in the data first. It will be followed by adapters trimming if needed. You can run RSeQC tool that can generate QC reports for data and other quality. I would also run multiQC to compile a QC report from all the QC tools above. Please Alignment QC Process.