Question: 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?
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gravatar for jonessara770
6 months ago by
jonessara770130
jonessara770130 wrote:

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

wes • 282 views
ADD COMMENTlink modified 6 months ago by Pierre Lindenbaum117k • written 6 months ago by jonessara770130
1
gravatar for Pierre Lindenbaum
6 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum117k wrote:

filter-in the single ends with samtools view -f 1 in.bam

1 is "read paired" https://broadinstitute.github.io/picard/explain-flags.html

ADD COMMENTlink modified 6 months ago • written 6 months ago by Pierre Lindenbaum117k
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