Extracting reference reads

User Support
1

Hi
I have a sample with read length of 250 bases. and while extracting reference reads, I chose min and the maximum length of 400 and 490 respectively. how this going to affect my downstream taxonomic and differential abundance analysis?

thanks
Nisha

2

Hi @Nisha,

Can you provide more details? What marker gene / variable region are you using? Are you using SILVA, GTDB, GreenGenes?

If your sequences are ~250 bp, then your minimum length should be below 250, not 400.

-Mike

3

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