Search found 181 matches

by wleung
Sat Sep 23, 2017 2:45 am
Forum: Annotation Questions
Topic: Altered Exon Structure and Missing Exon
Replies: 2
Views: 56

Re: Altered Exon Structure and Missing Exon

> At first, we thought it may be present on the next contig, but a BLAST search in FlyBase does not find any significant matches to [CDS] 15 The position of the D. eugracilis annotation projects are available through the "Annotation Projects" track on the D. eugracilis "April 2013 (BCM-HGSC/Deug_2.0...
by wleung
Sat Sep 23, 2017 2:41 am
Forum: Annotation Questions
Topic: Altered Exon Structure and Missing Exon
Replies: 2
Views: 56

Re: Altered Exon Structure and Missing Exon

> What evidence should we include to make the conclusion that part of these exons is not present in D. eugracilis? The strongest evidence which indicates that the 3' end of RhoGAP102A has changed in D. eugracilis is the D. eugracilis RNA-Seq data from the adult males, adult females, and mixed embryo...
by wleung
Wed Aug 30, 2017 6:01 am
Forum: GEP Web System Updates
Topic: Changes to the GEP Web Framework - Fall 2017
Replies: 0
Views: 59

Changes to the GEP Web Framework - Fall 2017

Changes to the GEP Web Framework - Fall 2017 Hello Everyone, The GEP Web Framework has been reset for the 2017 Fall semester. The key changes to the GEP Web Framework are summarized below: 1. Annotation projects for Fall 2017 3 D. ficusphila Muller D element projects and 2 D. eugracilis F element pr...
by wleung
Sat Jan 14, 2017 6:16 am
Forum: GEP Web System Updates
Topic: Changes to the GEP Web Framework - Spring 2017
Replies: 0
Views: 756

Changes to the GEP Web Framework - Spring 2017

Hello Everyone, The GEP Web Framework has been reset for the 2017 Spring semester. The projects with the highest priority are the annotation projects from the D. elegans and D. ficusphila Muller D elements, and the TSS projects from the D. biarmipes Muller F element. If you would like to incorporate...
by wleung
Tue Nov 29, 2016 9:10 pm
Forum: Annotation Questions
Topic: stop codon read-through
Replies: 1
Views: 294

Re: stop codon read-through

No. However, your students can include a note in the GEP Annotation Report after the screenshot of the Gene Model Checker checklist. The note will justify the error in the checklist with the explanation that the B isoform of Atox1 contains a read-through stop codon in D. melanogaster (see screenshot...
by wleung
Wed Aug 24, 2016 10:56 pm
Forum: GEP Web System Updates
Topic: Changes to the GEP Web Framework - Fall 2016
Replies: 0
Views: 721

Changes to the GEP Web Framework - Fall 2016

Hello Everyone, The GEP Web Framework has been reset for the 2016 Fall semester. During the Alumni Workshops this summer, we have discussed the revisions to the TSS annotation protocols and updates to the GEP Web Framework. (The presentations and curriculum materials from the Alumni Workshops are av...
by wleung
Sun Jun 19, 2016 10:41 pm
Forum: Frequently Asked Questions
Topic: Finding Finishing and Annotation Project Relationships
Replies: 1
Views: 292

Re: Finding Finishing and Annotation Project Relationships

The placements of the sequence improvement and annotation projects are available through the " Finishing Projects " and " Annotation Projects " tracks on the GEP UCSC Genome Browser (under the Assembly Tracks section. You can access the whole genome assemblies for the eight Drosophila species that h...
by wleung
Sat Jan 16, 2016 2:01 am
Forum: GEP Web System Updates
Topic: Changes to the GEP Web Framework - Spring 2016
Replies: 0
Views: 896

Changes to the GEP Web Framework - Spring 2016

Hello Everyone, We have reset the GEP Web Framework for the 2016 Spring semester. The list of key changes are summarized below: 1. Annotation projects for Spring 2016 46 D. elegans and one D. biarmipes Muller D element projects from Fall 2015 55 new annotation projects from the D. ficusphila Muller ...
by wleung
Thu Nov 05, 2015 9:07 pm
Forum: Sequence Improvement Questions
Topic: Mismatch correction using Illumina runs
Replies: 1
Views: 3203

Re: Mismatch correction using Illumina runs

Yes. I agree with your assessment that the high quality discrepancies can likely be attributed to Illumina reads that have been misplaced and that the consensus should not be changed. The region contain multiple blue (transposon) tags so some of the Illumina reads that have been mapped to this regio...
by wleung
Thu Oct 15, 2015 2:40 am
Forum: Sequence Improvement Questions
Topic: Inconsistent Read Pairs
Replies: 1
Views: 1152

Re: Inconsistent Read Pairs

> So, could these really be mismapped and there is an overlap that needs to be fixed. The high percent identity match could be due to multiple copies of a transposon (e.g. terminal repeats of an LTR retrotransposon). In this case, the region contains multiple helitron transposon fragments based on t...
by wleung
Tue Sep 15, 2015 2:30 pm
Forum: Sequence Improvement Questions
Topic: closing gaps without PCR
Replies: 3
Views: 1386

Re: closing gaps without PCR

> Is this a reasonable project to undertake? The primary sequence improvement goal for the hybrid assembly projects is to resolve consensus errors within mononucleotide runs. Resolving gaps and low quality regions are secondary goals for the project. It would be useful to have a more accurate estima...
by wleung
Tue Sep 15, 2015 4:31 am
Forum: Sequence Improvement Questions
Topic: closing gaps without PCR
Replies: 3
Views: 1386

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: 5324

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: 3666

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: 3666

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...