Search found 30 matches

by jstamm
Wed Apr 21, 2010 3:26 pm
Forum: Annotation Questions
Topic: Genes that are not covered within a single fosmid
Replies: 1
Views: 3089

Genes that are not covered within a single fosmid

Is it possible to see how two fosmids overlap? My student cannot find the next exon in the gene he is annotating (grimshawi fosmid 13, gene is zfh2) and we suspect that the intron might be so long that the next exon is not actually in his fosmid. I would like to look for overlap in the next fosmid o...
by jstamm
Wed Mar 03, 2010 4:13 pm
Forum: Sequence Improvement Questions
Topic: Tagging clone ends?
Replies: 3
Views: 5391

I noticed this last night (posted about this in the other post about not recognizing vector sequences) and was able to duplicate the effect today in other projects: The original ace files (ace.1) do not have any X's that indicate vector sequence. But if we run phredphrap, the new assemblies show the...
by jstamm
Wed Mar 03, 2010 1:42 am
Forum: Sequence Improvement Questions
Topic: Calling reads for really small problems
Replies: 1
Views: 3435

Calling reads for really small problems

I don't remember what to do with these: 1: This one looks like a clear high quality discrepancy. There is only one read that shows a T, all the others show a C. I don't think this is enough evidence to call it a polymorphism, so should we order a read for just this one base? Or do we just tag it (da...
by jstamm
Wed Mar 03, 2010 1:33 am
Forum: Sequence Improvement Questions
Topic: Vector sequence not recognized initially?
Replies: 1
Views: 3385

Vector sequence not recognized initially?

I've come across this twice now: First instance - my student started with this initial assembly: http://i67.photobucket.com/albums/h299/joycestamm/DMAC-12initialassemblyview.jpg There are repeated regions in the two contigs, so she looked to see if she could do a force join. She found a perfect matc...
by jstamm
Tue Mar 02, 2010 2:47 pm
Forum: Sequence Improvement Questions
Topic: Incorporating new reads
Replies: 1
Views: 3344

Incorporating new reads

(boy, I am full of questions. I don't remember being this lost last time.) I just looked on the Wiki, and it states that if you are using "Add New Reads" instead of phredphrap, that you should answer 'yes' to the question about putting new reads into their own contig if Consed can't put it into the ...
by jstamm
Tue Mar 02, 2010 1:18 pm
Forum: Sequence Improvement Questions
Topic: Tagging clone ends?
Replies: 3
Views: 5391

Tagging clone ends?

On the checklist, it states that we should tag the clone ends. In one of the tutorials, we were told to recognize clone ends by the presence of X's that indicate vector sequence. But in these projects we haven't come across any vector sequence. Should we still tag the clone ends, and if so, where sh...
by jstamm
Mon Mar 01, 2010 4:12 pm
Forum: Sequence Improvement Questions
Topic: Low consensus quality limit
Replies: 1
Views: 3118

Low consensus quality limit

I think I know the answer to this question, but just to be sure... The checklist states that the consensus bases need to have a quality of >25, unless the region is covered by a single subclone, in which case they need to have a quality of >30. What if we have a consensus base with quality = 28 or 2...
by jstamm
Mon Mar 01, 2010 4:08 pm
Forum: Sequence Improvement Questions
Topic: Dimmed high quality bases?
Replies: 1
Views: 3321

Dimmed high quality bases?

We came across this read, where the sequence was high quality (score in the 50s) but the sequence was dimmed, and the consensus was therefore given a low quality, since this was the only read in the region. http://i67.photobucket.com/albums/h299/joycestamm/dimmedhighqualitybases.png The student put ...
by jstamm
Fri Feb 19, 2010 6:16 pm
Forum: Sequence Improvement Questions
Topic: A bunch of discrepant reads...
Replies: 1
Views: 3292

A bunch of discrepant reads...

We have an assembly that looks like this: http://i67.photobucket.com/albums/h299/joycestamm/Contig23000-31202.jpg It looks to me like a misassembly in the repeat region. Can we just pull out the discrepant reads into their own contig (can someone remind me how to do this?) and then leave the ones th...
by jstamm
Tue Feb 16, 2010 12:26 pm
Forum: Sequence Improvement Questions
Topic: SNPs?
Replies: 1
Views: 3220

SNPs?

I was going through the "common problems with finishing" powerpoint prepared by Jeanette Wong with my students when I realized I don't really understand the two slides on SNPs. Here is the trace that she calls a polymorphism: http://i67.photobucket.com/albums/h299/joycestamm/SNP.jpg I assume that th...
by jstamm
Thu Feb 11, 2010 4:08 pm
Forum: Sequence Improvement Questions
Topic: Two contigs, one very short
Replies: 0
Views: 6886

Two contigs, one very short

I have a number of projects (DMAC-12a and DMAC-33b, for example) where I have a single large contig and then one small contig with only a few reads in it. This small contig contains fewer than 1000 bp. Also, at least for DMAC-12a, there appear to be tandem repeats in the 2 contigs, so that it would ...
by jstamm
Thu Feb 11, 2010 3:50 pm
Forum: Sequence Improvement Questions
Topic: Restriction digest is way off
Replies: 3
Views: 5204

I'm glad to see this (a year later). I have a student working with that fosmid this semester. We spent quite a bit of time puzzling over the digest before giving up. So this was never resolved?
by jstamm
Fri May 09, 2008 11:15 am
Forum: Annotation Questions
Topic: I am having problems with the Gene model checker
Replies: 2
Views: 3986

I am having problems with the Gene model checker

Everything works, but when I try to download the GFF file, I get this message:

Error: Invalid file path

I had a couple of students submit their stuff, so it worked for them, but it isn't working for this particular project, which is D. erecta contig 18.
by jstamm
Fri Apr 25, 2008 7:24 pm
Forum: Annotation Questions
Topic: alternative 5' UTR
Replies: 5
Views: 6450

Did you want the 5' UTRs in erecta annotated? I was working off the assumption that you only wanted coding sequences.
by jstamm
Thu Apr 24, 2008 1:33 pm
Forum: Annotation Questions
Topic: Annotation project report
Replies: 1
Views: 3045

Annotation project report

Is the report that needs to be submitted the form that was downloaded in the annotation packages?