Search found 67 matches

by drevie
Thu Mar 05, 2015 10:45 pm
Forum: Sequence Improvement Questions
Topic: Polymorphisms?
Replies: 1
Views: 3524

Polymorphisms?

In our D. elegans projects, we have a lot of cases where the 454 reads are almost entirely one sequence and the Illumina are almost entirely another. In most cases it is 10 or 20 differences in a stretch of 100 or so while in a couple its a stretch of 30-100 that are completely different (which look...
by drevie
Thu Feb 26, 2015 12:10 am
Forum: Sequence Improvement Questions
Topic: MNR in High quality discrepancy regions
Replies: 2
Views: 4354

Re: MNR in High quality discrepancy regions

I didn't think about problems with forced joins-I just assumed it was elsewhere. I'll ask them about that. Thanks.
by drevie
Wed Feb 25, 2015 4:48 pm
Forum: Sequence Improvement Questions
Topic: MNR in High quality discrepancy regions
Replies: 2
Views: 4354

MNR in High quality discrepancy regions

We are finishing DELE contigs. We have some regions where there are lots of HQD that also have MNR. Do we fix the consensus in the whole region, or just the repeats (T's in the picture-94620 and beyond). We have one or more other regions (other contigs) where the consensus and reads don't agree for ...
by drevie
Fri May 02, 2014 9:43 pm
Forum: Annotation Questions
Topic: Sequencing error?
Replies: 10
Views: 8084

Re: Sequencing error?

I think the confusion was when they put in PA, the browser showed them having an exon that wasn't in the browser PA model but instead was in the browser PC. They therefore retried it without that exon. For this gene, the browser is quite a bit off.

Thanks.
by drevie
Fri May 02, 2014 8:49 pm
Forum: Annotation Questions
Topic: Sequencing error?
Replies: 10
Views: 8084

Re: Sequencing error?

I guess the confusion is that the genome browser shows 4 exons, while the GeneModelChecker believes there are five for isoform A. The difference is apparently the third exon, which is in PC but not PA or PB (as seen in the browser). When all five exons are entered for PA, it passes the tests. Howeve...
by drevie
Fri May 02, 2014 4:14 am
Forum: Annotation Questions
Topic: Sequencing error?
Replies: 10
Views: 8084

Re: Sequencing error?

Sorry. Isoforms PA and PB are missing the middle exon, and this is the problem-the reading phase changes. Isoform PC uses three consecutive exons, including the two in your reply.
by drevie
Thu May 01, 2014 11:33 pm
Forum: Annotation Questions
Topic: Sequencing error?
Replies: 10
Views: 8084

Re: Sequencing error?

5' end of second exon
by drevie
Thu May 01, 2014 11:32 pm
Forum: Annotation Questions
Topic: Sequencing error?
Replies: 10
Views: 8084

Re: Sequencing error?

3' end conservation
by drevie
Thu May 01, 2014 11:13 pm
Forum: Annotation Questions
Topic: Sequencing error?
Replies: 10
Views: 8084

Re: Sequencing error?

3' end of first exon
by drevie
Thu May 01, 2014 11:02 pm
Forum: Annotation Questions
Topic: Sequencing error?
Replies: 10
Views: 8084

Re: Sequencing error?

3' end of first exon
by drevie
Thu May 01, 2014 11:00 pm
Forum: Annotation Questions
Topic: Sequencing error?
Replies: 10
Views: 8084

Sequencing error?

In annotating a gene, we have a case where there clear donor/acceptor sites for two exons, but the resulting peptide would have a frameshift. In looking at the end of the first exon, there are 5 As, but other Drosphila species have 4 As. Is this a sequencing error? (pictures below).
by drevie
Wed Apr 30, 2014 3:13 pm
Forum: Annotation Questions
Topic: Number of exons
Replies: 2
Views: 4447

Re: Number of exons

Thanks. I believe the problems are mostly between Flybase and GeneModelChecker, but the browser differences also occur. I've been telling them to double check all the differences in the dot plot, and ignore the warning if they have checked to make sure they don't have an extra or missing exon.
by drevie
Tue Apr 29, 2014 10:35 pm
Forum: Annotation Questions
Topic: Number of exons
Replies: 2
Views: 4447

Number of exons

In one or two cases, students seem to have found different numbers of exons shown by the browser, GeneModelChecker, and/or GeneRecordFinder. For example, the browser may show 4 exons and the GeneModelChecker expects 5. Is one of them slightly out of sync compared to the others regarding the D. melan...
by drevie
Thu Apr 24, 2014 8:46 pm
Forum: Annotation Questions
Topic: Annotate gene?
Replies: 1
Views: 3617

Annotate gene?

One contig has an exon with a match to the beginning of a RNA directed DNA polymerase of D. melanogaster (e 10-45). The gene is normally found in a retrotransposon transposable element, but RepeatMasker doesn't show it as a repeat. Is this because the repeats of D. biarmipes are enough different? Sh...
by drevie
Thu Apr 24, 2014 3:28 pm
Forum: Annotation Questions
Topic: New genes
Replies: 4
Views: 5350

Re: New genes

I believe there was also RNAseq evidence for it.