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The phrase "are excluded from downstream" is correct and usable in written English.
It can be used in contexts where certain items, processes, or individuals are not included in subsequent stages or processes.
Example: "Certain data sets are excluded from downstream analysis to ensure accuracy and relevance."
Alternatives: "are omitted from subsequent stages" or "are not included in later processes."
Exact(1)
The consequence of this is that when a gene finds a paralog as top BLAST hit instead of its ortholog, both the gene and its paralog are excluded from downstream analyses [ 67].
Similar(59)
Spots flagged as 'Not Found' by the GenePix algorithms were excluded from downstream analysis.
Occasionally, replicates gained significant turbidity, suggesting aerobic contamination of the hypoxic environment, and were excluded from downstream analysis.
These loci were excluded from downstream analyses.
Such clusters need to be excluded from downstream analysis.
These known germline SNPs were excluded from downstream analysis.
Duplicate reads were marked using Picard (http://picard.sourceforge.net/) and were excluded from downstream analyses.
During this process, the translocation, scramble and inversion reads were excluded from downstream analysis.
Samples tested positive for genomic DNA were excluded from downstream protocols.
For these reasons, these samples have been excluded from downstream analysis.
Duplicate reads, resulting from PCR clonality or optical duplicates, and reads mapping to multiple locations were excluded from downstream analysis.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com