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Old 02-11-2016, 12:04 PM   #1
Location: New York NY

Join Date: May 2015
Posts: 24
Default Enable pairing in a bam file separately aligned by lanes

Hi all,
I aligned paired end exome seq R1 and R2 fastq files separately as single end reads. Then I combined two resultant bam files using samtools cat and then sorted them by sequence.

However, this would obviously not enable pairing / not change the flags for paired reads.

Any suggestions how to enable pairing of the reads in the file ?
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