Search found 211 matches

by cshaffer
Fri Jan 24, 2014 5:18 pm
Forum: Sequence Improvement Questions
Topic: Hybrid Assemblies: criteria for HQDs in MNRs
Replies: 4
Views: 1160

Re: Hybrid Assemblies: criteria for HQDs in MNRs

Yes indeed, pretty horrible list with many many false positives. Finishing this type of assembly (i.e. a type we have never seen before), means that many computational tools that would help things run more efficiently have not yet been created. There is a bit of work on this from last fall; see the ...
by cshaffer
Mon Apr 15, 2013 6:22 pm
Forum: Annotation Questions
Topic: query regarding annotation word doc
Replies: 1
Views: 1003

Re: query regarding annotation word doc

Yes please, put all student names on the report, you can just edit as needed to add the extra names.
by cshaffer
Tue Feb 12, 2013 11:07 pm
Forum: Sequence Improvement Questions
Topic: Flybase BLAST vs. UCSC BLAT
Replies: 2
Views: 1186

Re: Flybase BLAST vs. UCSC BLAT

That message is consed warning the user that when consed tried to recognize which reads were of which type it looked like there are WAY to many "walking reads" (i.e. reads that come from a unique primer. Consed is giving the warning becuase it is probably more likely that there is an error in the na...
by cshaffer
Wed Feb 06, 2013 5:11 pm
Forum: Sequence Improvement Questions
Topic: Starting out from fosmid ends
Replies: 4
Views: 1202

Re: Starting out from fosmid ends

Oh another thought, not all end reads in a project are reads from that fosmid. There should be at least two other sets of end reads that come from the ends of the adjacent clones. The name of the end read includes "fosmidend" and then has the name of the template and a code for who did the sequencin...
by cshaffer
Wed Feb 06, 2013 3:33 am
Forum: Sequence Improvement Questions
Topic: Starting out from fosmid ends
Replies: 4
Views: 1202

Re: Starting out from fosmid ends

can you go back to the terminal and copy/paste the error message consed prints out. The message there is usually longer and more informative.
thanks
by cshaffer
Tue Feb 05, 2013 7:19 pm
Forum: Sequence Improvement Questions
Topic: Starting out from fosmid ends
Replies: 4
Views: 1202

Re: Starting out from fosmid ends

The basic Phrap protocol is to take each read individually and attempt to build an assembly, it starts with the reads that match most closely to each other and builds from there. There is no way I know of to tell Phrap the naming scheme for ends and ask it to do the assembly in the way you suggest (...
by cshaffer
Tue Feb 05, 2013 7:13 pm
Forum: Sequence Improvement Questions
Topic: pasting outside Consed?
Replies: 1
Views: 976

Re: pasting outside Consed?

Unix copy/paste is complicated. There is an X11 preference to try to keep the X11 "pasteboard" synchronized with the mac clipboard. Check the X11 preferences... "pasteboard"

of course for the consensus there is a work-around: export the consensus to a file and open with TextEdit then copy/paste.
by cshaffer
Tue Feb 05, 2013 7:05 pm
Forum: Sequence Improvement Questions
Topic: understanding fosmid end reads in the ananassae projects
Replies: 1
Views: 995

Re: understanding fosmid end reads in the ananassae projects

Yes the X's correspond to vector and should extend all the way, however the sequence quality can be so low that it no longer aligns with vector so the computer stops changing the bases to X's. The reads that span the fosmid end are from whole genome reads and retain the naming convention for genomic...
by cshaffer
Mon Jan 21, 2013 6:31 pm
Forum: Annotation Questions
Topic: Query regarding D ananassae projects
Replies: 1
Views: 1233

Re: Query regarding D ananassae projects

All very good questions, without seeing the exact evidence I cannot make any specific call but here are some general things to consider: First there will be some clones that at the end of the analysis one will have decided that there are no real genes in the clone. Unlike melanogaster, many of these...
by cshaffer
Mon Apr 02, 2012 12:34 pm
Forum: Annotation Questions
Topic: siz gene in fosmid 20 question
Replies: 3
Views: 1320

Re: siz gene in fosmid 20 question

It is certainly the case that we run across genes on occasion where one particular isoform from melanogaster is just not possible in the new species, even in species as close as D erecta. The fact that you are looking for the first exon makes this more complicated in that we find that small first ex...
by cshaffer
Wed Apr 06, 2011 5:49 pm
Forum: Annotation Questions
Topic: Adding Custom Tracks
Replies: 1
Views: 540

Re: Adding Custom Tracks

There is indeed a way to add custom tracks. To start the process you want to use the "add custom tracks" button on the genome gateway page to get to the upload page. Click the "genome browser" link on the front page to get to the genome gateway page. When you get to the upload custom tracks page you...
by cshaffer
Sat Feb 12, 2011 4:07 pm
Forum: Coming Meetings
Topic: Fly Meeting March 2011
Replies: 0
Views: 9071

Fly Meeting March 2011

The Drosophila meeting is coming up at the end of March! We will be sending the draft poster around soon. As previously discussed, Chris Shaffer will be the GEP staff representative at this meeting. We are in the process of arranging a room for us to meet at the conference site on Wednesday, March 3...
by cshaffer
Fri Feb 11, 2011 2:55 pm
Forum: Sequence Improvement Questions
Topic: all Ts in trace listed as Ns?
Replies: 1
Views: 1864

Re: all Ts in trace listed as Ns?

You are correct on all cases, except maybe the hallucination part. This is indeed an issue with the phred basecaller, not so much with more modern basecallers. This is almost always seen when there is a large dyeblob of T signal (due to a large amount of unincorporated dye-labeled ddTTP left in the ...
by cshaffer
Thu Jul 29, 2010 12:43 am
Forum: Annotation Questions
Topic: Question 3 in "A Simple Annotation Problem" handou
Replies: 2
Views: 651

Yes indeed, you are correct. When comparing sequences with each other (in NCBI blast) you need to click that little check box "Align two or more sequences". You will then get two input boxes one for each sequence. Bonus material for advanced users: you can actually put more than one sequence in eith...
by cshaffer
Tue May 25, 2010 5:17 pm
Forum: Alumni Workshop
Topic: June 2010 Alumni workshop
Replies: 4
Views: 5023

I have created a wiki page on the faculty only section of the wiki to post those items too large or cumbersome for inclusion here. The page is: http://gep.wustl.edu/restrictwiki/index.php/June_2010_Alumni_Workshop Since there have been several requests to add a introductory exercise on using Clustal...