Data Files
From OpenWetWare
Sequence files
- These are the quality-trimmed reads that did not have enough overlap to assemble (thus "frags").
- These are the quality-trimmed reads that did not have enough overlap to assemble and had a significant blast hit to the "left" side of a reference 16S sequence.
- These are the quality-trimmed reads that did not have enough overlap to assemble and had a significant blast hit to the "right" side of a reference 16S sequence.
- These are the reads that assembled into complete clones using the JGI's 16S pipeline (genelib).
- A fasta file of all the Clean Chimera-checked sequenced that were unclassified at the Genus level --James Angus Chandler 19:16, 24 April 2009 (EDT)
Taxonomy Assignments
- OLD, not quality-trimmed data: there are three files here, each corresponds to one of the three chimera-checked sequence files above (i.e., putative, sub-threshold, and clean)
- clean sequences File:Classifications All NAST.Bclean.fasta30593.xls
- sub-threshold chimeric sequences File:Classifications All NAST.Bambig.fasta27959.xls
- putative chimeric sequences File:Classifications All NAST.Bchimera.fasta28223.xls
Alignment
- below is the most current version of the NAST-formatted alignment file.
this is the older, not quality-trimmed file. It contains all of our sequences, plus the Corby-Harris and Cox-Gilmore sequences.
Environment File
Here is the environment file you asked for. Look it over to tell me if I need to add anything. I left ??? for the Cox-Gilmore samples since I cannot seem to find my copy of it and thus do not know what they collected over.
Media:MainEnvFile.xls --James Angus Chandler 20:45, 19 May 2009 (EDT)
Phylogenetic Tree
CalTech Presentation
Media:CalTech_Presentation.ppt --James Angus Chandler 00:56, 11 June 2009 (EDT)