will using samtools merge to multiple bam files also remove the redundancy ?
So i have merged some bam files using the samtools merge -n command, i wanna know if the merged bam file which is made now will be non redundant or do i have to again use bedtools to remove the redundancy ?
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GenoMax
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naveedhasan2000 •
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how do you define " redundancy" ? if both bams are unrelated, the merged bam won't contain any common read.
no the bams are not unrelated, they have common reads.
Are you talking about duplicate reads? If so, you can check the duplicates in your merged data simply by running-
As in they came from a single source sequence file and thus would have an identical fastq header?