Im working with paired-end RNA-seq data, and for my purpose I map the forward and reverse reads individually. What is the easiest way to assemle reads into a single alignment file while forcing the original direction to be preserved? So e.g. I want forward and reverse information of reads in final alignments.
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You know that aligners that make .sams will natively figure out how to combined your paired end data so that you still know which read cam from which fastq, right?
If you really have to work with these bams, set the flags yourself to indicate which come from read1, and which come from read 2, then merge the .bams.
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