my bam file contains both single-end and paired-end. How can I convert bam to fastq so that fastq contains only paired-end reads?
Hi
I have a bam file that contains both single and paired-reads. How can I convert bam to fastq so that fastq contains only paired-end reads?
Thanks
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Pierre Lindenbaum
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jonessara770
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jonessara770
1 answer
filter-in the single ends with samtools view -f 1 in.bam
1 is "read paired" https://broadinstitute.github.io/picard/explain-flags.html
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