RNA-Seq and ATAC-Seq quality check
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
• 895 views
•
link
updated
by
bk11 •
•
written
by
qudrat.nii •
•
written
by
qudrat.nii •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Machine learning for drug sensitivity prediction and signature gene
written by qudrat.nii •
-
Correlation for ATAC-Seq and Chip-Seq
written by qudrat.nii •
-
ATAC-Seq and featureCounts
written by qudrat.nii •
-
Single cell RNA vs ATAC seq
written by golden •
-
RNA-Seq QC for aligned files (bam)
written by genomics Newbie •
-
Differential Binding in Partek
written by DVA
-
Pre_processing BAM file for variant calling using RNA-seq data
written by ammarsabir15
-
which file to use for analysis
written by Learner
-
Differential gene expression using R studio
written by rachana.cdri •
-
Differential binding analysis
written by marina-orlova
I would start with
fastqcto check the quality of reads and any adapters present in the data first. It will be followed by adapters trimming if needed. You can runRSeQCtool that can generate QC reports for data and other quality. I would also runmultiQCto compile a QC report from all the QC tools above. Please Alignment QC Process.