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After trimming, we can conceivably have four fastq file types derived from a single original read pair:
- Trimmed forward reads with surviving reverse mate pairs
- Trimmed reverse reads with surviving forward mate pairs
- Trimmed forward reads without surviving reverse mate pairs
- Trimmed reverse reads without surviving forward mate pairs
Each of these read types would be useful to track independently for downstream applications -- for instance, in assembly or read mapping, type 1 and 2 above will frequently need to be provided in a set, while type 3 and 4 might optionally be concatenated and provided as independent single-ended reads.
Another scenario, when I'm doing HUMAnN2, I typically ignore reverse pairs altogether and only analyze Type 1 and Type 3 forward reads after trimming.
Suggest following names:
forward_trimmed_paired
reverse_trimmed_paired
forward_trimmed_unpaired
reverse_trimmed_unpaired
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