Can I submit assemblies with Ns inserted to estimate the length of the transcript?
TSA only accepts assemblies of overlapping reads or transcripts. We do not take sequences which have been assembled by inserting Ns, even of paired-ends. The only allowed Ns are internal Ns that represent ambiguous bases and this must follow the requirement that the total sequence be less than 10% n’s and the number of n’s in a row must be less than 15. Remove any Ns that are at the end of a assembly, and split an assembly into separate contigs at any Ns that represent gaps. Ns that represent gaps are not allowed, so sequences containing runs of Ns that represent gaps need to be split into individual assemblies. This is even true for sequences that were assembled by assemblers that connect mate-pairs.
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