Search found 8 matches

by espana
Mon Mar 15, 2010 5:11 pm
Forum: Sequence Improvement Questions
Topic: DMAC-40A & B sequence failures
Replies: 0
Views: 5215

DMAC-40A & B sequence failures

Hey all- We're working on DMAC-40A and so far every sequence we've done for this fosmid has failed: either giant blobs/peaks that can't be read or with just NNNN shown as the sequence in FinchTV. This is also the case for the sequences we've poached from the Elgin class (40A) and Stamm (40B). There ...
by espana
Mon Feb 01, 2010 6:21 pm
Forum: Installation Issues
Topic: OS X 10.6
Replies: 1
Views: 5067

OS X 10.6

I install the phred/phrap/consed package from GEP on student's macbooks if they are interested. I've had no problem with 10.4 or 10.5, but it appears that 10.6 doesn't actually have the "local" folder to put the genome folder into. Can I just make a "local" folder & put it in, or are there yet, stil...
by espana
Wed Feb 04, 2009 7:16 pm
Forum: Sequence Improvement Questions
Topic: Syntax error when trying to extract oligo sequences
Replies: 0
Views: 4278

Syntax error when trying to extract oligo sequences

Hi-Many students are having a syntax error when trying to extract oligo sequences for the second round of primer-calling. We get two different
errors: one is SyntaxError: parseJSON

What should we do?

eric
by espana
Thu Jan 15, 2009 2:15 pm
Forum: Installation Issues
Topic: Linux Installation
Replies: 0
Views: 5691

Linux Installation

Hi there- I'd like to install the consed package on a linux workstation I have sitting around. Do you folks have an installation package that would correspond to the version we are using on the macs? (The computer is running CentOS) I can get it directly from David Gordon, etc., but I was worried th...
by espana
Mon Nov 24, 2008 2:34 pm
Forum: Sequence Improvement Questions
Topic: Imported sequence doesn't match actual sequence
Replies: 1
Views: 485

and even weirder

If you look at the trace for the file in consed, if you look in the middle, the traces look fine, and the base call letters above it bear no resemblance to the trace below. if however you start looking at the trace in the first 20 nucleotides or so, it doesn't read any trace.

???
by espana
Mon Nov 24, 2008 2:25 pm
Forum: Sequence Improvement Questions
Topic: Imported sequence doesn't match actual sequence
Replies: 1
Views: 485

Imported sequence doesn't match actual sequence

We've gotten this twice now, with the same primer (which should close a gap): We get back the abi file, and open it in FinchTV, and it looks good. Nice peaks, good Q scores, essentially, no problems. We import it into consed via either phredPhrap or Add New Reads, and the sequence imported is differ...
by espana
Fri Nov 07, 2008 7:52 pm
Forum: Sequence Improvement Questions
Topic: phrap skipping reads
Replies: 1
Views: 482

phrap skipping reads

We tried adding 6 reads (that look great by FinchTV) via phredPhrap, and it put 5 in and skipped #6. Of course, #6 is the one that closes the gap! We can't get "Add new reads" to work, it seems to crash consed after giving a few different errors. Any good hints or reasons or any other options to sho...
by espana
Fri Aug 29, 2008 4:54 pm
Forum: Sequence Improvement Questions
Topic: crossmatch error
Replies: 18
Views: 1730

same crossmatch problem

Hi-
We just got essentially the same error message as the original post did on the same sample set but on a G4 Powerbook running OS 10.3.9. And then after that a problem with the add new reads command in the same tutorial. Any ideas?