Hi, I found the 454Isotigs.fna file contains many sequences that are 100% identical but with different lengths (i.e. one sequence contains another shorter one). Isn't this supposed not to happen. I mean they should be assembled as one? Thanks ...
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Originally posted by bioben View PostHi, I found the 454Isotigs.fna file contains many sequences that are 100% identical but with different lengths (i.e. one sequence contains another shorter one). Isn't this supposed not to happen. I mean they should be assembled as one? Thanks ...
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Thanks, kmcarr. I think you are right. Probably they are splicing variants.
Then how about singlets? I tried to find them back by parsing the 454ReadStatus.txt file. The resulting singlets file also contains many identical reads. To me, they are supposed to be assembled as one and show up in the isotigs file. Do people usually care about singlets or not? Thanks ...
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Originally posted by bioben View PostThen how about singlets? I tried to find them back by parsing the 454ReadStatus.txt file. The resulting singlets file also contains many identical reads. To me, they are supposed to be assembled as one and show up in the isotigs file. Do people usually care about singlets or not? Thanks ...
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Originally posted by westerman View PostI suspect that the singletons are not assembled together simply because they are identical and thus considered to be technical duplicates. It is hard to have a contig made up of exactly one identical read. If the reads overlap then they could be assembled. Unfortunately do not know of a 454 file that describes which reads are true singletons and which are duplicate singletons.
<minimumReadLength>45</minimumReadLength>
<overlapSeedStep>1</overlapSeedStep>
<overlapMinMatchLength>60</overlapMinMatchLength>
<overlapMinMatchIdentity>96</overlapMinMatchIdentity>
<ripMode>true</ripMode>
Make a new cDNA assembly, do not re-run it from the current assembly directory because in my opinion newbler does not re-compute the overlaps and hence not all changes will kick in. With these settings I got 50% more assembled contigs than with loose defaults!
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