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    Hello, do you mean you have a R1 and R2 file for every prefix (A1, A2, etc.)? Thx. Commented Feb 26, 2024 at 1:47
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    Do you need to explicitly match the prefixes, or can you simply take pairs of lines and place them side by side? If the latter, something like paste - - <yourfile would suffice. Commented Feb 26, 2024 at 1:49
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    Yes, @jubilatious1 sorry just edited the OG post, I have a R1 and R2 file for every prefix I need to match prefixes and put the two reads side by side Commented Feb 26, 2024 at 1:52
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    Does it matter whether A1_R1 comes before or after A1_R2 on the output line for that pair? Commented Feb 26, 2024 at 10:39
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    Does each of your pairs of associated _R1 and _R2 files come together in the listing, one immediately following the other? Commented Feb 28, 2024 at 15:45