Search found 185 matches

by wleung
Tue Sep 15, 2015 4:31 am
Forum: Sequence Improvement Questions
Topic: closing gaps without PCR
Replies: 3
Views: 7166

Re: closing gaps without PCR

> I assume you have to remove the DBIA read into its own contig to be able to close any gaps. Is this correct? Yes. Once you have removed the assembly piece (i.e. the DBIA read) from the assembly, I would recommend deleting the read from the assembly by selecting "Remove Reads" from the Consed Main ...
by wleung
Thu Aug 27, 2015 5:13 am
Forum: GEP Web System Updates
Topic: Changes to the GEP Web Framework - Fall 2015
Replies: 0
Views: 10606

Changes to the GEP Web Framework - Fall 2015

Hello Everyone, We have reset the GEP Web Framework for the 2015 Fall semester. The list of key changes are summarized below: 1. Annotation projects for Fall 2015 60 new annotation projects from the D. elegans Muller D element 11 annotation projects remaining from Spring 2015 (see below) 2. New tran...
by wleung
Mon Jul 06, 2015 3:30 pm
Forum: Beyond Annotation
Topic: modENCODE RNA-Seq data
Replies: 1
Views: 11006

Re: modENCODE RNA-Seq data

I am unaware of an existing list from modENCODE that shows the isoform expression levels of each D. melanogaster gene. I believe that all of the RNA-Seq information on FlyBase are summarized at the gene level (see the FlyBase RNA-Seq Release Notes ). You can download the RPKM values for all the D. m...
by wleung
Mon Jul 06, 2015 3:16 pm
Forum: Beyond Annotation
Topic: modENCODE RNA-Seq data
Replies: 1
Views: 11006

modENCODE RNA-Seq data

Question from Dr. Jamie Sanford, Ohio Northern University I am doing some basic gene expression analysis on my gene of interest. Specifically, we are trying to determine which of the gene's isoforms are expressed in fly ovary. Is there a way to easily use the modENCODE data to find out isoform spec...
by wleung
Mon Apr 06, 2015 11:22 pm
Forum: Annotation Questions
Topic: Annotation of UTRs?
Replies: 1
Views: 6818

Re: Annotation of UTRs?

The TSS annotations are optional for both the D. elegans and D. biarmipes projects. The current TSS annotation protocol recommends that your students should try to annotate the initial transcribed exon before trying to annotate the TSS. However, your students do not need to annotate all of the untra...
by wleung
Wed Mar 25, 2015 4:37 pm
Forum: Annotation Questions
Topic: Not all of the gene in the contig?
Replies: 1
Views: 4962

Re: Not all of the gene in the contig?

One approach that you can use to support the hypothesis that the project region only contains part of a gene is to show that the best match to the other coding exons (CDS) are located in the adjacent contigs. Because D. elegans is closely related to D. melanogaster , you can typically perform a BLAT...
by wleung
Tue Mar 17, 2015 1:30 am
Forum: Sequence Improvement Questions
Topic: final comment tag location?
Replies: 1
Views: 5688

Re: final comment tag location?

Please add the comment tag at the left end of the region analyzed by the student. For the hybrid assembly projects, this will usually correspond to the first base of the consensus sequence.
by wleung
Fri Mar 06, 2015 1:06 am
Forum: Sequence Improvement Questions
Topic: Polymorphisms?
Replies: 1
Views: 4730

Re: Polymorphisms?

As you have mentioned, unaligned high quality regions will frequently appear within genomic repeats in the hybrid assembly projects. In some cases, you can select " Tell phrap to not overlap reads at this location " at the discrepant positions and then perform a Miniassembly to create two separate c...
by wleung
Thu Mar 05, 2015 4:36 pm
Forum: Annotation Questions
Topic: unconventional start codons
Replies: 2
Views: 6368

Re: unconventional start codons

As you have mentioned, the FlyBase comments for the Wnk gene models indicate that this gene uses a non-canonical start codon (AUU). The comment also indicates that this non-canonical start codon is conserved in other Drosophila species. alternate_start_codon_comment.png Examination of the "Conservat...
by wleung
Wed Feb 25, 2015 5:03 pm
Forum: Sequence Improvement Questions
Topic: MNR in High quality discrepancy regions
Replies: 2
Views: 5878

Re: MNR in High quality discrepancy regions

This type of discrepancies typically appears after you have removed reads (or did a tear and join) from a region. In some cases, Consed did not recalculate the consensus correctly and it uses a much lower quality read in the region as the consensus. These regions would need to be resolved prior to p...
by wleung
Thu Feb 19, 2015 7:15 am
Forum: Sequence Improvement Questions
Topic: inserting bases into the consensus?
Replies: 1
Views: 4830

Re: inserting bases into the consensus?

One way you can insert a new base into the consensus is by inserting the base into one of the reads aligned to the position of interests and then change the consensus. Basically, you can open one of the traces and then select the base just after where you want to add a base in the "edt" line. Press ...
by wleung
Mon Jan 12, 2015 12:56 am
Forum: GEP Web System Updates
Topic: Changes to the GEP Web Framework - Spring 2015
Replies: 0
Views: 8776

Changes to the GEP Web Framework - Spring 2015

Hello Everyone, We have reset the GEP Web Framework for the 2015 Spring semester. The list of key changes are summarized below: 1. Annotation projects for Spring 2015 Projects from the D. biarmipes Muller D element and the D. elegans Muller F element Optional annotation of transcription start sites ...
by wleung
Fri Dec 12, 2014 3:33 am
Forum: Annotation Questions
Topic: Premature Stop codons
Replies: 1
Views: 5292

Re: Premature Stop codons

> We are having multiple troubles with premature stop codons... Especially the last exon of many genes. As a reminder, the "Coding Exon Coordinates" field should not include the stop codon. If the issue persists, please verify that the splice sites of adjacent exons have compatible phase (see descri...
by wleung
Tue Oct 21, 2014 11:08 pm
Forum: Annotation Questions
Topic: Discrepancies for some isoforms
Replies: 2
Views: 5676

Re: Discrepancies for some isoforms

The available evidence suggests that the initial CDS of the E and F isoforms of the M6 gene (CDS 2_7735_0) might not exist in D. biarmipes . However, based on parsimony (i.e. minimize the number of changes compared to D. melanogaster ), I would annotate the CDS 2_7735_0 in D. biarmipes based on the ...
by wleung
Thu Sep 25, 2014 5:31 pm
Forum: Sequence Improvement Questions
Topic: High number HQDs - only one run matches consensu
Replies: 5
Views: 7505

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. Yes. Unfortunately, we do not have any external evidence (e.g., restriction digests, long high quality reads) that would convince a reviewer that the edits that we have made to the assembli...