Search found 47 matches

by chauser
Wed Feb 26, 2014 1:37 am
Forum: Sequence Improvement Questions
Topic: Misassemblies
Replies: 1
Views: 5160

Misassemblies

Several students have what appear to be missassemblies that are indicated by blocks of HQD flanked by blocks of aligned sequence.
We are tagging these as possible misassemblies, but I really want to rip those reads out.
Since no restriction map, my understanding is to leave them in - correct?

Chuck
by chauser
Wed Feb 19, 2014 1:41 am
Forum: Sequence Improvement Questions
Topic: Error loading ace for primers
Replies: 2
Views: 5673

Error loading ace for primers

When trying to extract oligos from the ace file, I get the follow error:

g[this.contig] is undefined

The previous ace file, if selected gives the error: no oligos selected--which is correct.
by chauser
Tue Feb 11, 2014 11:56 pm
Forum: Sequence Improvement Questions
Topic: HYbrid Assemblies: inconsistent read pairs
Replies: 1
Views: 4445

HYbrid Assemblies: inconsistent read pairs

GEPers

In the hybrid assemblies, it would seem that the inconsistent read pairs warning (red triangles) "to far apart size compared to lib max" would not apply as there is no library?

Or, are these warnings to be ignored, or are they reflecting the size of the illumina reads?

Chuck
by chauser
Fri Jan 24, 2014 1:17 am
Forum: Sequence Improvement Questions
Topic: Hybrid Assemblies: criteria for HQDs in MNRs
Replies: 4
Views: 8480

Hybrid Assemblies: criteria for HQDs in MNRs

We are looking thru the search features of consed to find regions that match all 3 criteria: HQ >40 >= 3 HQDs MNR >=5 Under Navigate by HD regions we can specify # discrepant read =3 ignore bases below qual=40 but this returns MANY reads that are not in MNRs We need a custome sort/search - suggestio...
by chauser
Mon Apr 19, 2010 10:24 pm
Forum: Annotation Questions
Topic: Gene model checker
Replies: 0
Views: 7163

Gene model checker

Any chance there is an error (off by one) in how gene model checker is translating? We have several instances where we are confident in the splice site, but when the coords are run through the checker, the splice sites pass - all green, but when you look at the translated seq, it is reading in the w...
by chauser
Wed Mar 10, 2010 2:21 pm
Forum: Sequence Improvement Questions
Topic: fake reads
Replies: 0
Views: 7623

fake reads

Chris, We have a project that still has a gap DGA38L22 (we'll see if reads today close it). We decided to try to make a fake read to either design primers from, or to close the gap itself. -blasted 2 contigs vs grimshawii (flybase) -identified grimshawii scaffold coordinates that span the gap -pulle...
by chauser
Mon Mar 08, 2010 10:09 pm
Forum: Sequence Improvement Questions
Topic: reads ordered
Replies: 1
Views: 4847

reads ordered

DGA38L22.20 DGA38L22.19 Student ordered reads for these two primers on 2.24.10 using Big Dye with dGTP. When looking in the project management system they are not showing up. Reads with these primers were ordered before with 4:1 chemistry. Can you tell if these primers are being used in the current ...
by chauser
Wed Mar 03, 2010 11:11 pm
Forum: Sequence Improvement Questions
Topic: additional digests DMAC-48A
Replies: 2
Views: 6252

additional digests DMAC-48A

Chris,

Are additional digests available for DMAC-48A other than those that came with the project?
We have a couple of frags present in in-silco absent in real that look real.

Chuck
by chauser
Tue Feb 23, 2010 3:23 pm
Forum: Sequence Improvement Questions
Topic: restriction frag
Replies: 1
Views: 3811

restriction frag

Question regarding an EcoRI digest. Digests suggest that EcoRI site at 5172 should not be present. However, when the student looked into this, there is a read that spans this site (5172) and one to the right at 5857. The catch is that this read ends ~ 5885 and qual is dropping, and that what should ...
by chauser
Tue Feb 23, 2010 12:05 pm
Forum: Sequence Improvement Questions
Topic: Short Joined Contig
Replies: 2
Views: 4857

Chris, Zane added up the "real digests" and received the following total fragment lengths and the sizes are pretty scattered. Digest Sums (Actual): EcoRV = 37,329 bp EcoRI = 35,261 bp SacI = 29,413 bp HindIII = 32,576 bp So, EcoRV comes in at ~ 37-10 vector which suggests 28 for insert would be clos...
by chauser
Tue Feb 23, 2010 11:54 am
Forum: Sequence Improvement Questions
Topic: Sequence compressions?
Replies: 2
Views: 4860

Chris, It appears the pads are due to reads that are out of 'phase'. In the cases I looked at, the broad peaks are at the beginning of the read, and the peaks tighten up as you get farther into the read. So, I don't think these are polymorphisms or misassemblies. In this case so long as the consensu...
by chauser
Thu Feb 18, 2010 5:47 pm
Forum: Sequence Improvement Questions
Topic: Sequence compressions?
Replies: 2
Views: 4860

Sequence compressions?

We have a project where what appears to be a sequence compressions problem ? is generating an erroneous consensus.

Are these compressions?
Suggestions for dealing with this?

Chuck

Image
by chauser
Wed Feb 17, 2010 11:31 pm
Forum: Sequence Improvement Questions
Topic: Short Joined Contig
Replies: 2
Views: 4857

Short Joined Contig

I am working on contig DGA19A15, and I have joined all of my sub-contigs together. The problem is that their combined length is 28.3 kb, which is far less than the 40 kb expected length. I am thinking that this represents a misassembly. Any chance a fosmid could be ~28 kb?

-Zane Goodwin
by chauser
Wed Mar 11, 2009 7:18 pm
Forum: Sequence Improvement Questions
Topic: Contig SIze
Replies: 3
Views: 5465

Chris,

the project is DGA19A15.

Chuck
by chauser
Sun Mar 08, 2009 10:14 pm
Forum: Sequence Improvement Questions
Topic: Contig SIze
Replies: 3
Views: 5465

Contig SIze

Have a contig that totals to ~27kb where as the real digest total to ~35kb. Is it a fair assumption that we are missing data from an unspanned gap? - mis-assembly by the whole genome shotgun assembly ? Chuck http://i161.photobucket.com/albums/t238/charlesh_02/ace33contigsize.png http://i161.photobuc...