Comments (1)
ollenordesjo
commented on September 24, 2024
Hi @avilella, sorry for the delay in replying
Yes, that's correct, by default it will go to what the --output_dir is set to. The reason for this is to keep the associated files together (both the paired ids without the filtering, and also the filtered ids). Note that you would typically want to use the filtered pair ids for downstream analysis. If there are any reads missing, it's always possible to reconstruct expected pairs from either the pair_stats file (which has some additional metrics), or by the pair_ids.txt file (if you are ok with some false positives).
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Related Issues (20)
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