I used newbler 2.6 with the -scaffold option and hope I can use the paired end fosmid library sequences (insert size is around 30-40kb) to produce some scaffolds. It did produced some scaffold files but no of them are really scaffolds. They are exactly the same as the contigs. In another word, all the scaffold only contain one contig.
I have total around 6753 paires in total of 13506 reads of the fosmid sanger sequences.
When I look at the 454PairStatus.txt file, all the paired sequence' status under the following situation: BothUnmapped, OneUnMapped, NoThreshold.
One I examine the NoThreshold ones, they are all mapped to different contigs.
I could not find any things which refer to NoThreshold in the manure. Could anyone give me some hints?
I have total around 6753 paires in total of 13506 reads of the fosmid sanger sequences.
When I look at the 454PairStatus.txt file, all the paired sequence' status under the following situation: BothUnmapped, OneUnMapped, NoThreshold.
One I examine the NoThreshold ones, they are all mapped to different contigs.
I could not find any things which refer to NoThreshold in the manure. Could anyone give me some hints?
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