Description of phredPhrap output files

February 18, 2008 at 7:28 am (bioinformatics, consed, phrap, phred, software) (, , , , , )

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.screen
test.screen.out
test.fasta.log — contains this line “No. words: 509136; after pruning: 497472”
test.fasta.screen.singlets
test.fasta.screen.contigs
test.fasta.screen.view
test.fasta.screen.contigs.qual — quality file for test.fasta.screen.contigs
test.fasta.screen.ace.1 — ace file for consed to read
test.phrap.out
test.fasta.screen.log
test.fasta.screen.problems
test.fasta.screen.problems.qual
test.contigs — fasta seq of all the contigs
test_to_alu.cross
test.contigs.log — contains this line “No. words: 169360; after pruning: 166242”
test.newtags

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Alternative tutorial to phred/phrap/consed

December 10, 2007 at 9:33 am (consed, phrap, phred) ()

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

http://cse.fra.affrc.go.jp/ksaitoh/using_consed-e.html

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