Search found 211 matches

by cshaffer
Mon May 17, 2010 3:11 pm
Forum: Alumni Workshop
Topic: June 2010 Alumni workshop
Replies: 4
Views: 31777

Dear colleagues, We need to review and revise our templates for gathering data on how we are using GEP materials ( instructors form ) and for gathering data on our institutions ( intro & inst survey form ). These forms were used to gather data for the CBE paper (Shaffer et al 2010), and data of this...
by cshaffer
Mon May 17, 2010 12:52 pm
Forum: Alumni Workshop
Topic: June 2010 Alumni workshop
Replies: 4
Views: 31777

re:ModEncode

Sally's response: Thanks for your note. We have just posted our new “tour” on next-generation sequencing on the website! You can access this from the bottom of the center panel on the home page. This illustrates how the Illumina and 454 sequencing technologies work, and the impact on sequencing cost...
by cshaffer
Mon May 17, 2010 12:51 pm
Forum: Alumni Workshop
Topic: June 2010 Alumni workshop
Replies: 4
Views: 31777

first topic - modEncode

Alexis Nagengast sent this in: Is there any way we could get a primer on deep sequencing or how to access and use the modENCODE data? I haven't had time to figure out how to do it myself but I think a little lesson could go along way and I'd like to incorporate it into my classes. Thanks, Alexis Ale...
by cshaffer
Mon May 17, 2010 12:49 pm
Forum: Alumni Workshop
Topic: June 2010 Alumni workshop
Replies: 4
Views: 31777

June 2010 Alumni workshop

This thread is for documents and discussion of topics to be covered in the Alumni workshop scheduled for June 4th -6th.

Please post your thoughts here for all to see – join the dialogue, regardless of whether you will be able to attend, so we have the broadest possible input!
by cshaffer
Mon May 03, 2010 1:46 pm
Forum: Annotation Questions
Topic: Genes that are not covered within a single fosmid
Replies: 1
Views: 6100

Fosmid locations

sorry for the late reply, this is the last week of classes here and it has everyone very busy. Go the the gep wiki and click on current projects. Once there click on the project for that students. On that page there are links to genome browser pages with each fosmid mapped to the larger scaffold. Th...
by cshaffer
Thu Mar 04, 2010 1:42 pm
Forum: Sequence Improvement Questions
Topic: additional digests DMAC-48A
Replies: 2
Views: 10271

The DMAC series does not have any extra digests. The missing/extra bands can occur by the computer mis-calling the bands. We have software to look at the raw data (gel images) to see if there was a likely mis-call but its unix-only and complicated to install. The best thing to do is get in touch wit...
by cshaffer
Wed Mar 03, 2010 6:56 pm
Forum: Sequence Improvement Questions
Topic: Vector sequence not recognized initially?
Replies: 1
Views: 6439

it looks like the initial assemblies where made without the correct vector file. Usually this does not matter as there are no vector sequences in the production reads. Notice from the different name pattern that the two reads that eventually got X'ed out are not production reads these are actually e...
by cshaffer
Wed Mar 03, 2010 6:37 pm
Forum: Sequence Improvement Questions
Topic: Calling reads for really small problems
Replies: 1
Views: 6459

1. in this case just tag it with a comment, it is either a polymorphism or a mutation that occured during growth, no way to know which so we just comment them. Clearly the consensus should be C that's what matters most. We only want to tag polymorphisms if there is good evidence and you are convince...
by cshaffer
Wed Mar 03, 2010 6:24 pm
Forum: Sequence Improvement Questions
Topic: Incorporating new reads
Replies: 1
Views: 6382

sorry to say life and science are often messy and rarely aesthetically pleasing. It is not terrible to leave them out but sometimes even if the computer cannot incorporate them a human can. Remember that you know where the oligo is so you have a strong prediction of its location. In rare cases the l...
by cshaffer
Tue Mar 02, 2010 11:53 am
Forum: Sequence Improvement Questions
Topic: Low consensus quality limit
Replies: 1
Views: 6148

There is an official "escape clause" in the published standard for the mouse genome which is what we are trying to meet. It the mouse standard one way to meet the standard is to "be approved by an experienced finisher". This is really exactly for situations like this. The data clearly supports the c...
by cshaffer
Wed Feb 24, 2010 7:18 pm
Forum: Sequence Improvement Questions
Topic: restriction frag
Replies: 1
Views: 6354

can you explain in more details what is going on with the digest? Is it simply that there is a band missing in the real digest that you expect based on the in silico? Or rather is there an unmatched band in the real digest that would match the sum of the two predicted bands on each side of the 5172 ...
by cshaffer
Mon Feb 22, 2010 6:01 pm
Forum: Sequence Improvement Questions
Topic: Short Joined Contig
Replies: 2
Views: 8365

yes this size is possible but not common. Of the 84 clones analyzed in detail for consideration into which would be sequenced I found 3 that were smaller than 33 kb. What do your digests look like? What is the sum of all the fragments called in the "real" digests. Do all the enzymes report about the...
by cshaffer
Mon Feb 22, 2010 5:48 pm
Forum: Sequence Improvement Questions
Topic: Sequence compressions?
Replies: 2
Views: 8353

This is not a compression, a compression is the same base repeated two or more times in a row in which you get fewer peaks than the real number of bases. For example you have 2 G's in a row that "compress" into a single peak that is often subtly larger and fatter. All the reads you are showing look ...
by cshaffer
Mon Feb 22, 2010 1:53 pm
Forum: Sequence Improvement Questions
Topic: A bunch of discrepant reads...
Replies: 1
Views: 6325

These are tricky, since we have about 1/2 and 1/2 this could be reads that indicate polymorphisms or it could misassembly of a repeat. The first thing to do is check your read pairs, use the "find reads containing" box in the main window, you can search with the main read name and see if there are t...
by cshaffer
Wed Feb 17, 2010 3:26 pm
Forum: Sequence Improvement Questions
Topic: SNPs?
Replies: 1
Views: 6251

I am not convinced is slide 10 that the area she is highlighting is correctly tagged as a polymorphism. Of course there could be more reads in this region that support the polymorphism call here but if I only had only these two reads shown I would not call it a polymorphism. The "double peaks" you s...