Checking bam quality

Question

[Gene_MMP8]

I have multiple bam files from cancer datasets and I want to check their quality. What I did was, I converted the bam to fastq using bedtools. I got two fastq read files (paired end) per bam file. Now I checked the quality of the fastq files generated using fastqc tool. This is how I am trying the find a good dataset for my analysis. Is this approach ok?

Answer 1

[venu]

No. It's not ok.

You are checking the quality of fastq file but what you want is BAM quality. There is a difference between two. Check Qualimap to assess the quality of aligned BAM.

If it is ChIP-seq data, explore deepTools. It has very nice functions.

[Gene_MMP8]

Thanks for your reply. I get your point. Let me rephrase. So now I have only bam files and I want to check the fastq quality of the files that produced these bam files, then is the above method ok?

[venu]

You can directly run fastqc on bam files to get fastq quality. Skip time consuming BAM -> fastq.

[Gene_MMP8]

But my reads are paired end. So to check quality of both reads, I need to make read 1 and read 2 for each bam file and then check it using fastqc tool. Isn't it?

[finswimmer]

So to check quality of both reads

Please define what you mean by "quality". There are so many things one can look for and it maybe depends on the goal of your analysis.

fin swimmer

[Gene_MMP8]

Per base sequence quality