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amplicon_pipeline_readme [2014/10/03 01:25] dave [What we provide] |
amplicon_pipeline_readme [2015/05/14 06:16] 127.0.0.1 external edit |
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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: | ||
| Line 22: | Line 22: | ||
| * Representative Sequence | * Representative Sequence | ||
| - | The processing statistics file contains the following columns for each sample: | + | The processing statistics file (jobid_run_statistics.csv) contains the following columns for each sample: |
| * Sample | * Sample | ||
| * Total Read Count R1 | * Total Read Count R1 | ||
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| * Reads in complete OTU table R1 | * Reads in complete OTU table R1 | ||
| * Reads in filtered OTU table (>0.05% abundance) R1 | * Reads in filtered OTU table (>0.05% abundance) R1 | ||
| - | |||
| Kind Regards, | Kind Regards, | ||
| The ACE Team | The ACE Team | ||
