trying to figure out the output files in edit_dir.. this post will be a post in progress will update as and when i have new information
basically this is a list of files that I have when i run phredPhrap as a package where test is the default project/folder name.. the below files are created in top to bottom order
testNewChromats.fof — list of the chromatogram reads that are used in phredPhrap from the start.
test.fasta — suspect its fasta seq output from phd2fasta script from the phd files created by phred in phd_dir
test.fasta.screen.qual — suspect its quality file output from phd2fasta script from the phd files created by phred in phd_dir
test.fasta.log — contains this line “No. words: 509136; after pruning: 497472”
test.fasta.screen.contigs.qual — quality file for test.fasta.screen.contigs
test.fasta.screen.ace.1 — ace file for consed to read
test.contigs — fasta seq of all the contigs
test.contigs.log — contains this line “No. words: 169360; after pruning: 166242”
Found that someone else posted another manual for the set of tools.
nice to cross reference when you don’t get what the original manual is trying to say