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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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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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