Update UPARSE_workflow_97clust_v1.5_usearch_64bits_no_singletons_pear…

…_BayesHammer.sh
ramalok · May 1, 2016 · 7c9988d · 7c9988d
1 parent e2df4b7
commit 7c9988d
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/UPARSE_workflow_97clust_v1.5_usearch_64bits_no_singletons_pear_BayesHammer.sh b/UPARSE_workflow_97clust_v1.5_usearch_64bits_no_singletons_pear_BayesHammer.sh
@@ -265,9 +265,12 @@ echo "5) Labeling OTU repseq"
 
 python $scripts/fasta_number.py otus97_repset_nochimera.fa OTU_ > otus97_repset_clean.fa
 
-echo "6) Map all reads (including singletons) back to OTUs. Using -maxhits 1 -maxaccepts 20 -maxrejects 50000 for higher sensitivity. Adjust -threads to your resources"
+echo "6) Mapping all reads back to OTUs" 
 
-$usearch -usearch_global $reads -db otus97_repset_clean.fa -strand plus -id 0.97 -uc map97.uc -maxhits 1 -maxaccepts 20 -maxrejects 50000 -threads 24
+## Using -maxhits 1 -maxaccepts 20 -maxrejects 5000 for higher sensitivity. Adjust -threads to your resources
+## As a rule of thumb, the -maxrejects value should be similar to the number of sequences in "otus97_repset_clean.fa"
+
+$usearch -usearch_global $reads -db otus97_repset_clean.fa -strand plus -id 0.97 -uc map97.uc -maxhits 1 -maxaccepts 20 -maxrejects 5000 -threads 24
 
 echo "7) Generate OTU table"