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lotus [2019/09/13 02:44]
telatina
lotus [2019/09/13 03:00] (current)
telatina
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 ===== Preliminary analysis ===== ===== Preliminary analysis =====
  
-Before running the lOTUs pipeline, that is automatic, we can manually perform some steps to better understand how the input data is manipulated.+Before running the lOTUs pipeline, that is automatic, we can manually perform some steps to better understand how the input data is manipulated. ​To keep the procedure simple
  
 ==== Merge R1 and R2 ==== ==== Merge R1 and R2 ====
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 gunzip *.gz gunzip *.gz
 usearch -fastq_mergepairs *R1* -relabel @ -fastq_maxdiffs 20 -fastq_pctid 80 -fastqout merge.fq usearch -fastq_mergepairs *R1* -relabel @ -fastq_maxdiffs 20 -fastq_pctid 80 -fastqout merge.fq
-</​code> ​+</​code>​ 
 + 
 +The program will print the number of pairs merged, and the reason why some pairs weren'​t merged at all (usually too many errors).  
 + 
 +===== Using lOTUs ===== 
 + 
 +==== Preparing the mapping file ==== 
 +The first step for most 16S analysis pipelines it to prepare a file connecting the files to some form of sample identifier. Lotus provides a script to prepare a minimal mapping file. 
 + 
 +<​code>​ 
 +autoMap.pl  
 +</​code>​