Bam quality vs read quality

[bong28]

I have a cancer bam file and want to check its read qualities. I have two options in mind.
1. Check bam quality through fastqc
2. Convert the bam file into paired-end reads (in fastq) and check their quality in fastqc.
Are both the processes equivalent?

[GenoMax]

Yes, because FastQC is a QC program. FastQC does not modify raw data. It is going to show you summary of the same Q-scores whether they come from the BAM or the fastq reads extracted from the BAM file.

[bong28]

Sorry for the late followup to your reply. If that is the case, then why am I getting poorer quality when I convert the bam to 2 fastq files(read 1 and 2) whereas good quality when just checking the bam file as a whole?

[iEugene8]

Probably, there is the problem with sorting. (check https://twitter.com/davisjmcc/status/931298649841188864 )