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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...

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...

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...

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...

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 ...

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 ...

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...

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 ...

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.

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...

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...

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...

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...

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...

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.