Search found 185 matches

by wleung
Thu Feb 28, 2013 4:27 pm
Forum: Sequence Improvement Questions
Topic: phrap ignoring "do not overlap" command
Replies: 1
Views: 8418

Re: phrap ignoring "do not overlap" command

The fact that phrap attempts to join the region you have tagged as "do not overlap" suggests the region have very high degree of similarity. This could mean that the discrepancy could be a polymorphism instead of a misassembly. To force phrap to not overlap a region, you can make more of the discrep...
by wleung
Thu Feb 28, 2013 4:10 pm
Forum: Sequence Improvement Questions
Topic: What to do with a contig that doesn't fit
Replies: 3
Views: 12693

Re: What to do with a contig that doesn't fit

In many projects, there are usually extra reads that are left over besides the main contig. These are often low quality reads or possible contamination. Generally you can ignore these extra reads if the main contig passes the finishing standard (e.g. digests are consistent and there are no inconsist...
by wleung
Thu Feb 28, 2013 12:02 am
Forum: Annotation Questions
Topic: Anananasee annotation -missing , extra exons
Replies: 3
Views: 11752

Re: Anananasee annotation -missing , extra exons

Compared to D. erecta , genes in D. ananassae are less similar to genes in D. melanogaster . Consequently, BLAST might report multiple alignment blocks for a single exon because only parts of the exon is conserved with D. melanogaster . In these cases, you would still annotate the region as a single...
by wleung
Tue Feb 26, 2013 4:40 pm
Forum: Sequence Improvement Questions
Topic: high-frequency peaks?
Replies: 1
Views: 8149

Re: high-frequency peaks?

The "high frequency" peaks is an artifact of the "Display traces for all reads" function in Consed. The "Display traces for all reads" function tries to scale all the reads to the same horizontal scale. Consequently, in the case where there are deleted bases in some of the reads (i.e. danafos7163.g1...
by wleung
Mon Feb 25, 2013 11:28 pm
Forum: Annotation Questions
Topic: Annotation report form - isoform naming
Replies: 1
Views: 8041

Re: Annotation report form - isoform naming

If the coding sequences are identical among the different isoforms, you only need to include the analysis of one of the isoforms in the annotation report. However, you should include the GFF, transcript and peptide sequence files for all isoforms irrespectively of whether the coding regions are the ...
by wleung
Thu Feb 21, 2013 6:14 am
Forum: Sequence Improvement Questions
Topic: What to do with a contig that doesn't fit
Replies: 3
Views: 12693

Re: What to do with a contig that doesn't fit

In many cases, the extra reads are placed in a repetitive region with a blue transposon tag. This suggests that these reads might have been derived from a different copy of a transposon in the genome and the reads were misplaced in the published draft assembly. I would recommend pulling these reads ...
by wleung
Thu Feb 21, 2013 6:05 am
Forum: Sequence Improvement Questions
Topic: Fixing high quality discrepancies with change to low quality
Replies: 1
Views: 7357

Re: Fixing high quality discrepancies with change to low qua

For highly repetitive projects, multiple unaligned high quality reads might indicate that the project contains a a misassembly. However, if examination of the unaligned high quality regions indicate that the discrepancies are in fact low quality, you can simply add a comment tag to indicate that you...
by wleung
Tue Feb 19, 2013 12:35 am
Forum: Sequence Improvement Questions
Topic: What is the difference between a putative and potential SNP?
Replies: 1
Views: 11725

Re: What is the difference between a putative and potential

In most cases, we cannot confirm that a single nucleotide polymorphism (SNP) is genuine without doing additional sequencing on a population. However, we can often distinguish strong SNP candidates from weaker ones based on the number of high quality reads that shared the same allele. For strong SNP ...
by wleung
Sat Feb 16, 2013 6:04 am
Forum: Annotation Questions
Topic: Problem in annotating D.ananassae fosmid
Replies: 4
Views: 14285

Re: Problem in annotating D.ananassae fosmid

Yes, you could use the Gene Model Checker to verify partial genes. In this case, you could select the Partial option under the "Completeness of Gene Model Translation" field and then select Missing 3' end of translated region under the "Region Missing" field.
partial_gene_3prime_end.png
check partial gene using the Gene Model Checker
partial_gene_3prime_end.png (16.59 KiB) Viewed 14279 times
by wleung
Thu Feb 14, 2013 11:04 pm
Forum: Annotation Questions
Topic: Problem in annotating D.ananassae fosmid
Replies: 4
Views: 14285

Re: Problem in annotating D.ananassae fosmid

Based on your description of the problem, I assume you are trying to annotate the SPoCk gene at the beginning of fosmid_1145J01 in D. ananassae fosmid_1145J01_begin.png Genes that are near the beginning or the end of the fosmids are often incomplete. Because the fosmid insert corresponds to a random...
by wleung
Thu Feb 14, 2013 3:35 am
Forum: Sequence Improvement Questions
Topic: "Unaligned high quality" must not mean what I think it means
Replies: 1
Views: 7404

Re: "Unaligned high quality" must not mean what I think it m

Because the spurious unaligned high quality reads do not usually affect the consensus, the best way to resolve the issue is by either changing the low quality bases to N's or to add a comment tag indicating that the unaligned region is low quality. However, if you see green matchElsewhereHighQual ta...
by wleung
Tue Feb 12, 2013 6:51 pm
Forum: Annotation Questions
Topic: Which projects to claim?
Replies: 2
Views: 9624

Re: Which projects to claim?

Because most of the D. biarmipes projects have been claimed more than twice, I would recommend working on the D. ananassae projects. > What guidelines should we use for claiming projects - in terms of times claimed and times submitted? If possible, please focus on projects that have not yet been cla...
by wleung
Tue Feb 12, 2013 5:19 am
Forum: Sequence Improvement Questions
Topic: Flybase BLAST vs. UCSC BLAT
Replies: 2
Views: 10721

Re: Flybase BLAST vs. UCSC BLAT

There are a few possible reasons why the fosmid end reads cannot be mapped by BLAT. First, the D. ananassae genome assembly on the gander server is incomplete. Consequently, you should use the BLAT service at the official UCSC Genome Browser when performing BLAT searches against the whole genome ass...
by wleung
Tue Feb 12, 2013 1:24 am
Forum: Sequence Improvement Questions
Topic: good digest, (some) bad read pairs
Replies: 3
Views: 18522

Re: good digest, (some) bad read pairs

I do not believe there is an easier way to export the sequences of individual reads using Consed. However, in addition to pulling the reads out and exporting the consensus, there are two additional ways you can use to obtain the sequence of individual reads in a Consed database: 1. Use a trace viewe...
by wleung
Thu Feb 07, 2013 4:01 pm
Forum: Sequence Improvement Questions
Topic: Fosmid placement map
Replies: 3
Views: 11118

Re: Fosmid placement map

The direct links to the D. ananassae fosmid placement maps are also available on the GEP wiki under Current Research Projects. You can find the links to the three scaffolds we are currently working on under the Drosophila ananassae dot chromosome page.