Save Toner when printing from Consed output!

August 22, 2008 at 2:49 am (bioinformatics, consed, software, tips)

finally found the answer here from this helpful site!


There is a free (or nearly free) program called “xv”. One web site is It is written by one of those dying breed of
UNIX programmers who just *loved* UNIX and programming and sharing it.
His web site is enjoyable because some of his passion comes through.
With xv, you can make a postscript file from a Consed window. Then
you can print the postscript file on a color printer.

However, since some Consed windows are mostly black (Aligned Reads
Window and Traces Window), this uses up a lot of toner and is
difficult to read. So go to the Consed Main Window, pulldown the
‘Options’ menu and release on ‘General Preferences’. Scroll down to
“Make light background in Aligned Reads Window…” and click on “Do it
now”. Dismiss any Aligned Reads Windows or Traces Windows and then
bring them back up. You will notice the light background. A few
other things (traces colors and thickness) are also customized for
making color prints.


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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.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”

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resizing windows consed changing background for printing

December 12, 2007 at 8:20 am (consed) ()

Fed up with resizing consed windows each time i open the prog. trying to look into consedrc to see if i can make it remember windows sizes

stumble upon with these sites with no info for my purpose but might be helpful for u

interesting stuff on the last link to change BG of the windows for environmentally frenly slides printing

if you wish to edit consedrc

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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

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View all your subclone insert size in consed

December 6, 2007 at 7:13 am (consed) (, , , , , , )

the consistency in the sizes of the subclones is an important information in assembly. Up till today I used a calculator to calculate the sizes of the insert when i need to resolve some mis-assembly issues. Then I figured, phrap has to calculate the insert size somewhere to know that they are consistent! after going through the menus for a good 5 min i found what I want under the quite misleading name “Template Insert Locations”

Consed Main Window-> Info -> Show Template Insert Locations

it doesn’t not show where your subclones are in the contigs

instead it shows ‘insert size’ ‘sequencing position of the start of the insert in universal primer read’ and if ‘this template is ok to be used by autofinish’

This information is useful for me to double check some iffy regions whether phrap assembled the region wrongly.

for one thing I still can’t figure out how phrap determines if the insert size is ‘consistent’ or inconsistent…. can’t find this in the help manual.

if you know anything can you contact me?

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