Search found 28 matches

by dpaetkau
Sun Jun 19, 2016 6:48 pm
Forum: Frequently Asked Questions
Topic: Finding Finishing and Annotation Project Relationships
Replies: 1
Views: 217

Finding Finishing and Annotation Project Relationships

Hello Wilson,

How do you find a graphical relationship between the finishing and annotation projects for the same region.

Don
by dpaetkau
Mon Nov 02, 2015 5:50 pm
Forum: Sequence Improvement Questions
Topic: Mismatch correction using Illumina runs
Replies: 1
Views: 3135

Mismatch correction using Illumina runs

Hello, I would like to ask a question to be sure that we are finishing according to the current best practices. I have a student that was wondering if the following logic is correct: There was a HQD found at position 19117 on contig 1495012. It seems from the evidence of the Illumina reads that the ...
by dpaetkau
Thu Oct 15, 2015 1:33 am
Forum: Sequence Improvement Questions
Topic: Inconsistent Read Pairs
Replies: 1
Views: 1103

Inconsistent Read Pairs

Hello All Knowing Forum Participants, I have an interesting case for you finishers. Actually two similar cases. The first is project DBIA1495015. As you can see by the first picture, there is a whole set of inconsistent read pairs due to distance between the end reads exceeding the expected distance...
by dpaetkau
Tue Sep 15, 2015 1:22 pm
Forum: Sequence Improvement Questions
Topic: closing gaps without PCR
Replies: 3
Views: 1319

Re: closing gaps without PCR

Thank you for the clear answer. As a follow up and to complete the discussion for others that are attempting PCR: Is this a reasonable project to undertake? In other words, would it be a good idea to try a longer PCR/Sanger reads to fix this miss-assembly/inversion, or is the chance of being success...
by dpaetkau
Tue Sep 15, 2015 1:58 am
Forum: Sequence Improvement Questions
Topic: closing gaps without PCR
Replies: 3
Views: 1319

closing gaps without PCR

I am wondering how to close gaps without PCR. I assume you have to remove the DBIA read into its own config to be able to close any gaps. Is this correct? Particularly, I am working on DBIA2377007. The red triangles seems to indicate that there is a problem in the area of the gap. To be able to tear...
by dpaetkau
Thu Dec 11, 2014 7:45 pm
Forum: Annotation Questions
Topic: Premature Stop codons
Replies: 1
Views: 1202

Premature Stop codons

Hello Wilson, We are having multiple troubles with premature stop codons showing up in many of our gene model checkers. Especially the last exon of many genes. I thought I knew how to do this and when I check the phases between the two exons, they are right. So here is another example of even weirde...
by dpaetkau
Thu Sep 25, 2014 2:29 pm
Forum: Sequence Improvement Questions
Topic: High number HQDs - only one run matches consensu
Replies: 5
Views: 1080

Re: High number HQDs - only one run matches consensu

It seems to me that your explanation is also the reason that we are not focusing on HQDs in non-MNR regions. My students (and I will admit that I too am guilty), have got a bit caught up in these problems. They are both interesting and frustrating. What I hear you telling us in your last post is tha...
by dpaetkau
Tue Sep 23, 2014 5:01 pm
Forum: Sequence Improvement Questions
Topic: PCR Primer Extraction
Replies: 2
Views: 1016

Re: PCR Primer Extraction

Thank you Wilson,

Now that I look back at the command, I see my very silly mistake. I appreciate you putting up with all of our silly questions.
by dpaetkau
Tue Sep 23, 2014 5:00 pm
Forum: Sequence Improvement Questions
Topic: High number HQDs - only one run matches consensu
Replies: 5
Views: 1080

Re: High number HQDs - only one run matches consensu

Hello Wilson, I completely understand the first paragraph and that makes sense that we want to easily identify changes. It seems to me that your last line suggests that the consensus is more reliable (since it takes into account end reads, for example) than the Consed arrangement. My problem is a th...
by dpaetkau
Tue Sep 23, 2014 2:12 pm
Forum: Sequence Improvement Questions
Topic: High number HQDs - only one run matches consensu
Replies: 5
Views: 1080

High number HQDs - only one run matches consensu

Hello, We are encountering a interesting phenomenon in some projects - a spot where every run except one disagrees with the consensus. At first we thought that it was a Baylor mistake - the only run that has the different base is the one named for the project name, and so it just means the original ...
by dpaetkau
Tue Sep 23, 2014 2:01 pm
Forum: Sequence Improvement Questions
Topic: PCR Primer Extraction
Replies: 2
Views: 1016

PCR Primer Extraction

Hello All, I am having trouble using the aceNOligos.perl line to extract PCR primers from the ace file. (where N = latest ace file number). So, here is what I did. Opened DBIA1412001 in consed. Located the low consensus quality region at about 23100 (I chose this as an example and don't really care ...
by dpaetkau
Mon Jul 14, 2014 7:32 pm
Forum: Sequence Improvement Questions
Topic: Maps of all Annotation and Finishing Projects
Replies: 1
Views: 915

Maps of all Annotation and Finishing Projects

How do you find a map of all of the current finishing projects and annotation projects for D, biarmipes?
by dpaetkau
Mon May 20, 2013 2:39 pm
Forum: Sequence Improvement Questions
Topic: Trouble submitting a finishing project
Replies: 1
Views: 972

Trouble submitting a finishing project

We are trying to submit a project and we keep getting the following message at the end of a long interval of waiting. Any ideas why it might be happening? I have opened the students Checklist and Zipped file and re-saved and re-compressed them on my Mac to see if that would work, and it doesn't. The...
by dpaetkau
Thu May 02, 2013 7:08 pm
Forum: Annotation Questions
Topic: Submitting Annotation report for a gene desert fosmid
Replies: 1
Views: 933

Submitting Annotation report for a gene desert fosmid

I am trying to submit several of our projects that are gene deserts. Students have performed the 3 tests for a gene desert and they have all passed those tests. The problem is in submission. There are no pep, fasta or gff files for a gene desert project. The submission causes an error if you attach ...
by dpaetkau
Thu Feb 21, 2013 4:42 am
Forum: Sequence Improvement Questions
Topic: What to do with a contig that doesn't fit
Replies: 3
Views: 1213

What to do with a contig that doesn't fit

I have a couple of students with projects that seem to have reads (a small contig) that don't belong to their project. The evidence for the readings being in the wrong project includes very good restriction digest evidence for the contig without the extra reads and either (1 project) a large increas...