Comments (3)
lentendu
commented on July 2, 2024
In GitLab by @lentendu on Feb 7, 2018, 16:02
- configuration parameter "ITSx region to extract"
- set variable "ITSX"
- variable possible values: no (default) / ITS1 / ITS2 (values for the ITSx option --save_regions)
- to place in the trim step after trimming, dereplication, pre-clustering and chimera removal
- disable the length truncation for 454 reads (no keepfirst option in trim.seqs, no -t in FlowClus) if only ITS1 or ITS2 region is extracted
- warning for the documentation: better not use with cd-hit-est clustering if only ITS1 or ITS2 region is extracted because those regions are highly variable in size and cd-hit-est always sort longest reads first, with the consequence that the first read used to create OTU seeds will not be the most abundant.
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lentendu
commented on July 2, 2024
In GitLab by @lentendu on Mar 21, 2018, 18:20
mentioned in commit d29b00b
from deltamp.
lentendu
commented on July 2, 2024
In GitLab by @lentendu on Mar 22, 2018, 13:44
mentioned in commit dc8fcd4
from deltamp.
Related Issues (20)
- Adapt raw stat R scripts to R 4
- Avoid error if all reads already used in one direction for bidirectionnal libraries
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- Add header option to mimato
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- Allow disabling DADA2 bimera removal HOT 1
- Problem with restart from step when cut_db in the steps
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- Feature: similarity based clustering for pair-end sequences which cannot be assembled
- Feature: provide manually curated reference sequences to use for taxonomic identification
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- Change minimum number of rank depending on database for cut_db
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