Originally posted by aliceb
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Second, I used Tablet to view the alignment of my raw 454 reads as they are aligned into contigs and isotigs (454Isotigs.ace). I have a lot of things that are just called contigs, which means that they belong to an isogroup with only one sequence in it, right (i.e. Newbler didn't detect any evidence of splice variants in this 'gene')?
Contigs are added to the ace file when they are not used for isotigs, for various reasons explained in my post. I would check the fasta header for that contig in the 454AllContigs.fna file, it will report the 'status', and when that is not 'isotig', it indicates why the contig did not make it into an isotig. Also, check how many contigs belong to this isogroup...
The worry-some thing here is that some of these individual alignments are really bad (see attached Screenshot copy.jpg). I haven't given Newbler anything shorter than 100bp, and yet it has assembled many short sequences together. Doesn't this seem strange?
Hope this helps...
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