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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
The text was updated successfully, but these errors were encountered:
After trimming, we can conceivably have four fastq file types derived from a single original read pair:
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
The text was updated successfully, but these errors were encountered: