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Update Practical 3 Processing 16S rRNA amplicon data authored by Taylor Priest's avatar Taylor Priest
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Practical-3-Processing-16S-rRNA-amplicon-data.md
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...@@ -63,7 +63,7 @@ Next, we want to make file paths for the filtering and trimming step that will b ...@@ -63,7 +63,7 @@ Next, we want to make file paths for the filtering and trimming step that will b
Now we move on to actually filtering and quality trimming our reads. Again use `?` to see what filterAndTrim does, and what the various options are here. Although we will later only use the forward reads, we will still trim forward and reverse as pairs!!! Now we move on to actually filtering and quality trimming our reads. Again use `?` to see what filterAndTrim does, and what the various options are here. Although we will later only use the forward reads, we will still trim forward and reverse as pairs!!!
```plaintext ```plaintext
> filtered_out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs, maxN=0, maxEE=c(5,5), compress=TRUE, multithread=8) > filtered_out <- filterAndTrim(fnFs, filtFs, fnRs, filtRs, maxN=0, maxEE=c(5,5), compress=TRUE, multithread=8, minLen=100)
``` ```
What is maxEE? Feel free to try out other options like truncQ and truncLen to see if they change the output. What is maxEE? Feel free to try out other options like truncQ and truncLen to see if they change the output.
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