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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