Hi. I have paired end reads (75 bp) from a Nextseq run. Read 1 is 18 bp and Read 2 is 52 bp. R2 is where all the cDNA information is, and R1 is UMI (8) and Barcode (10bp). I've already run
umi_tools to detect the UMIs and append those to read file info (https://github.com/CGATOxford/UMI-tools). So R1 now just has the 10 bp barcode left. I think the most efficient way is to take that 10 bp barcode and join it directly to the R2 read on the 5' end. Then I can take the joined R2+R1 fastqs through a program like
reaper to demultiplex based on barcodes.
So my question is, what tool can I use for a simple join like that? I've seen tools like ea-utils that seem to do a join and merge based on overlapping bps between R1 and R2, but that's not what I want. I just want to add R1 to R2, no merge or overlap. Any guidance would be great.