Your Inner Fish
Hmm must make it a point to read this book
there’s a vid of the author being interviewed on the Colbert Report at Logsdon’s post and also check out Pharyngula’s post on it
Description of phredPhrap output files
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
Next Gen sequencing technology
What bioinformatics do you do?
nsaunders has nicely summarised the categories of bioinformatics here
you must also read Mike’s amusing post, World of Bioinformatics Quest: Character generation that describes characters in the lab like MMORPG game char!
on a related note check out Mastering Your Phd
Artemis: a DNA sequence viewer and annotation tool
there are so many tools for molecular biologists out there. that its not surprising to find a hidden gem that’s how i feel about artemis.
check it out! I think its invaluable for sequence annotation
