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amplicon_pipeline_readme [2014/10/03 01:16]
dave [What we provide]
amplicon_pipeline_readme [2014/10/03 01:26]
dave [What we provide]
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 Fasta files are processed using [[http://​qiime.org|QIIME'​s]] pick_open_reference_otus.py workflow with default parameters (97% similarity) and taxonomy assignment and alignment features suppressed. The resulting OTU table is filtered to remove any OTU with an abundance of less than 0.05%. Representative OTU sequences are then BLASTed against the reference database ([[http://​greengenes.lbl.gov/​cgi-bin/​nph-index.cgi|Greengenes]] version 2013/05 for 16S, [[http://​www.arb-silva.de|Silva]] version 119 for LSU, and [[http://​unite.ut.ee|UNITE]] singleton included release 04/07/2014 for fungal ITS amplicons). The main analysis output is an OTU table comprising the taxonomic classification of the best database match and a representative sequence for each OTU. Fasta files are processed using [[http://​qiime.org|QIIME'​s]] pick_open_reference_otus.py workflow with default parameters (97% similarity) and taxonomy assignment and alignment features suppressed. The resulting OTU table is filtered to remove any OTU with an abundance of less than 0.05%. Representative OTU sequences are then BLASTed against the reference database ([[http://​greengenes.lbl.gov/​cgi-bin/​nph-index.cgi|Greengenes]] version 2013/05 for 16S, [[http://​www.arb-silva.de|Silva]] version 119 for LSU, and [[http://​unite.ut.ee|UNITE]] singleton included release 04/07/2014 for fungal ITS amplicons). The main analysis output is an OTU table comprising the taxonomic classification of the best database match and a representative sequence for each OTU.
 ====What we provide==== ====What we provide====
-We provide the fastqc reports, trimmed fasta sequences, OTU tables (QIIME BIOM file, a filtered raw count table, and a filtered fraction table), processing statistics, and a file listing software versions from the QIIME pipeline.+We provide the fastqc reports, trimmed fasta sequences, OTU tables (QIIME BIOM file, a filtered raw count table, and a filtered fraction table), processing statistics ​file and associated bar plot, and a file listing software versions from the QIIME pipeline.
  
 The count and fraction OTU tables have the following columns: The count and fraction OTU tables have the following columns:
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   * Representative Sequence   * Representative Sequence
  
 +The processing statistics file (jobid_run_statistics.csv) contains the following columns for each sample: 
 +  * Sample 
 +  * Total Read Count R1 
 +  * Total Read Count R2 
 +  * Reads Passing QC R1 
 +  * Reads Passing QC R2 
 +  * QIIME pre-filtered reads R1 (reads with < 60% match to any sequence in the database) 
 +  * QIIME unclustered singletons R1 (reads that do not cluster with any other reads) 
 +  * Reads in complete OTU table R1 
 +  * Reads in filtered OTU table (>0.05% abundance) R1
  
 Kind Regards, Kind Regards,
 The ACE Team The ACE Team
amplicon_pipeline_readme.txt · Last modified: 2016/02/03 04:08 by brian
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