Bam to fastq conversion
I have a bam file from a cancer dataset and I want to convert it to FASTQ to check its quality. So I use this command samtools fastq #bamfile > cancer.fa. I intend to use this fastq file as an input to the FASTQC tool and get an idea about its quality. But these are paired end reads. So how can I get two read files (fastq) separately,(from a bam file) ? Is it ok to proceed with only one fastq file instead of two(for paired end reads) for quality analysis?
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FASTQC can not handle paired-end data, and thus only works on separate files (treating forward and reverse read as two independent reads)
see also here: Is Paired End analysis possible with FASTQC