Search found 185 matches

by wleung
Thu Apr 10, 2014 12:57 am
Forum: Annotation Questions
Topic: Frame disagreement between browser and Blastx alignments
Replies: 4
Views: 6657

Re: Frame disagreement between browser and Blastx alignments

Unfortunately, I could not reproduce the discrepancy. The blastx search of the CDS plexB:6_1762_0 against contig1 shows that the match is in frame -2, consistent with the results shown on the GEP UCSC Genome Browser: blx_plexB_6_17862_0_contig1.png One possible explanation for the discrepancy is tha...
by wleung
Thu Apr 10, 2014 12:40 am
Forum: Annotation Questions
Topic: Exon location
Replies: 4
Views: 6394

Re: Exon location

Both proposed hypothesis are possible but I could not ascertain which hypothesis is more likely without examining the region in the genome browser and gather more evidence. In general, non-canonical GC donor sites are found in ~1% of Drosophila genes. Consequently, we will annotate a GC donor site i...
by wleung
Thu Apr 10, 2014 12:23 am
Forum: Annotation Questions
Topic: Very short first exon
Replies: 1
Views: 4743

Re: Very short first exon

In general, I would recommend using the RNA-Seq data (particularly the TopHat junctions and the the Alignment Summary tracks) to help you identify small coding exons. The Annotation Strategy Guide contains an example (starting on page 17) that illustrates how you can use the RNA-Seq data to identify...
by wleung
Wed Feb 26, 2014 2:31 am
Forum: Sequence Improvement Questions
Topic: Misassemblies
Replies: 1
Views: 4617

Re: Misassemblies

Yes, your students do not need to resolve the misassembled regions unless they are near gaps or contains low quality data. You can simply add a comment or "doNotFinish" tag to regions that might contain a misassembly. Because of the small number of paired end reads with large insert sizes and the la...
by wleung
Thu Feb 20, 2014 9:07 pm
Forum: Sequence Improvement Questions
Topic: Error loading ace for primers
Replies: 2
Views: 4937

Re: Error loading ace for primers

Thanks for sending me the ace file. I have patched the Project Management System so that it should now correctly handle hybrid assemblies with multiple tear and joins. Please let me know if you encounter any additional issues submitting the ace files with the oligos. Thanks again for letting me know...
by wleung
Wed Feb 19, 2014 7:03 am
Forum: Sequence Improvement Questions
Topic: Error loading ace for primers
Replies: 2
Views: 4937

Re: Error loading ace for primers

The error message indicates that one of the contig tags in the D. biarmipes assembly is missing from the ace file. Please email the ace file you are trying to upload to me so that I can try to reproduce the problem. If possible, please let me know the web browser and the operating system you are usi...
by wleung
Fri Feb 14, 2014 12:59 am
Forum: Sequence Improvement Questions
Topic: PCR
Replies: 1
Views: 3855

Re: PCR

As Chris mentioned in page 4 of the Sequence Improvement Protocol for GEP Hybrid Assembly Projects document, our initial assessment of the D. biarmipes projects suggest regions with low consensus quality are rare because of the high 454 and Illumina read coverage. The low consensus quality regions a...
by wleung
Wed Feb 12, 2014 2:10 am
Forum: Sequence Improvement Questions
Topic: HYbrid Assemblies: inconsistent read pairs
Replies: 1
Views: 3908

Re: HYbrid Assemblies: inconsistent read pairs

While the "inconsistent read pairs" warning is correct, resolving misassemblies is beyond the scope of the current D. biarmipes sequence improvement project. The Illumina reads for the D. biarmipes are paired end reads with a total length of 250bp. A subset (9 out of 19) 454 GS FLX Titanium runs for...
by wleung
Mon Jan 27, 2014 5:02 pm
Forum: Sequence Improvement Questions
Topic: Hybrid Assemblies: criteria for HQDs in MNRs
Replies: 4
Views: 7322

Re: Hybrid Assemblies: criteria for HQDs in MNRs

Sorry about the delay in posting the revised curriculum materials for sequence improvement of the hybrid assemblies. You can find the updated and new curriculum materials for improving the modENCODE hybrid assemblies using the " Hybrid assembly " tag on the GEP web site. Most of the new curriculum m...
by wleung
Fri Jan 24, 2014 1:31 am
Forum: Sequence Improvement Questions
Topic: Hybrid Assemblies: criteria for HQDs in MNRs
Replies: 4
Views: 7322

Re: Hybrid Assemblies: criteria for HQDs in MNRs

Unfortunately, the current recommendation is to manually identify the mononucleotide run (MNR) regions that overlap with the highly discrepant regions. Basically, you can perform a "Search for String" for "AAAAA" and "GGGGG" to generate the list of MNR regions. Then you can compare the list of MNR r...
by wleung
Tue Jan 14, 2014 12:41 am
Forum: GEP Web System Updates
Topic: Changes to the GEP Web Framework - Spring 2014
Replies: 0
Views: 9200

Changes to the GEP Web Framework - Spring 2014

The GEP web framework has been reset for the 2014 Spring semester. For annotation, we will continue to work on annotation projects from the D. biarmipes Muller F element and the D. ananassae Muller D element. While all the annotation projects have been claimed multiple times in Fall 2013, only a sma...
by wleung
Tue Sep 24, 2013 5:43 pm
Forum: Annotation Questions
Topic: different frame between BLAST results and genome browser
Replies: 2
Views: 5515

Re: different frame between BLAST results and genome browser

There were two sequencing errors in Thd1 that have been fixed in the Aug. 2013 assembly. The BLAST results suggests that you might be using the previous version of the assembly which contains the sequencing errors and the frame shifts in the last CDS of Thd1 . I just performed the BLASTX alignment o...
by wleung
Fri Aug 23, 2013 2:05 am
Forum: GEP Web System Updates
Topic: Changes to the GEP Web Framework - Fall 2013
Replies: 0
Views: 8249

Changes to the GEP Web Framework - Fall 2013

Hello Everyone, The GEP web framework has been reset for the 2013 fall semester. Summary of key changes New annotation projects from the D. biarmipes Muller F element and the D. ananassae Muller D element New protocol for identifying and documenting potential consensus errors in the D. biarmipes ass...
by wleung
Wed May 22, 2013 12:14 am
Forum: Sequence Improvement Questions
Topic: Trouble submitting a finishing project
Replies: 1
Views: 3875

Re: Trouble submitting a finishing project

Please logout of the Project Management System, login and try submitting the project again. When transferring large projects, the file upload sometimes get interrupted and results in a partial file upload. This issue can typically be solved by logging out and submitting the project again. Please let...
by wleung
Mon May 13, 2013 10:06 pm
Forum: Annotation Questions
Topic: claimed same project twice...
Replies: 2
Views: 5453

Re: claimed same project twice...

Yes. We will reset the Project Management System before the fall semester so the duplicate claims is not a problem. Some GEP faculty members will claim the same projects multiple times and assign them to students in different sections. Consequently, the Project Management System allows the same facu...