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Old 03-29-2018, 10:28 AM   #1
bong28
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Default Bam quality vs read quality

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?
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Old 03-29-2018, 04:39 PM   #2
GenoMax
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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.
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Old 04-03-2018, 08:58 AM   #3
bong28
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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?
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Old 04-03-2018, 10:44 PM   #4
iEugene8
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Probably, there is the problem with sorting. (check https://twitter.com/davisjmcc/status/931298649841188864 )
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