Description of Standard Directory Structure


  • Picture of directory structure
  • 
    Standard Directories:
    
    These are all needed to run phred, phrap, consed and polyphred.
    
    edit_dir - used when running phredPhrap or phredPhrapPoly
               used when running consed
               *.ace files generated by phrap stored here
               "global assembly" directory
               
    chromat_dir - chromatogram files stored here
                  chromatogram files moved here, renamed and compressed by running move_chromats
                      from the new_chromats directory
                  chromatogram files should be compressed (*.gz)
                  
    phd_dir - phred sequence files stored here (*.phd)
              reference sequence stored here (*.reference.phd.1)
              
    poly_dir - polyphred files stored here (*.poly)
               polyphred files generated by phred
               
               
    Alternative Directories (Nickerson Laboratory)
    
    analysis_dir - top level directory used for "local/queried assemblies"
    
    	The directories in analysis_dir mimic the top-level standard directories described above:
    
    	edit_dir - used when running vp
    	           used when runnnig consed_edit
    	           *.ace files generated by phrap
    	           "local assembly" directory
    	           
    	chromat_dir - queried chromatogram files
    	              linked to top-level chromat_dir
    	             
    	phd_dir - queried *.phd files
    	          linked to top-level phd_dir
    	          files copied back to top-level phd_dir when terminating vp or consed_edit
    	          
    	poly_dir - queried *.poly files
    	           linked to top-level poly_dir
    	          
    
    new_chromats - storage area for new chromatogram files
                   used for running move_chromats
                   move_chromats will rename, compress, and move chromatograms to chromat_dir
                   all unanalyzed files should be kept here
                   
    bad_chromats - "bad" (low quality) chromatograms stored here
                   "misaligned" chromatograms
                   "questionable" chromatograms
                   Note: never delete a chromatogram - store it here
                   
    fasta_dir - contains all fasta files needed for analysis
                *.reference.fasta
                other misc. fasta files needed to create reference
                *.primers.fasta - all primers selected from reference sequence
                                  all primers should be listed with universal sequence when used
                *.cdna.fasta - mRNA sequence for gene of interest including UTR sequence
                *.exons.fasta - fasta file with multiple entries for each gene exon
                
    drawmap_dir - files needed to generate DrawMap output files stored here
                  *.repeats.xm - generated by RepeatMasker
                  *.primers.xm - cross_match output of *.primers.fasta against your *.reference.fasta
                  *.exons.xm - cross_match output of *.exons.fasta against your *.reference.fasta
                  *.variants.txt - table file used by DrawMap
                  *.list - file listing inputs to DrawMap
                  
                  Output file from DrawMap:
                  *.drawmap.ps
                  
    stats_dir - files generated from the database extraction (sq4polyphred), hapinf, 2hap
                Database extraction files:
                *.prettybase.txt
                *.hw.txt
                *.hz.txt
                *.freq.txt
                *.lde.txt
                
                hapinf output files:
                *.haps.txt
                *.phased.prettybase.txt
                *.phased.samples.txt
                *.unphased.samples.txt
                  
                2hap output file:
                *.dnadist.txt
                *.drawtree.ps
                *.neighbor.txt