Hi,
this is possibly a dumb question, but if my goal is to find siRNA (20-25 nt long) why are the Illumina reads 36 nt long, at least before quality trim? if a 24 nt long RNA piece (plus primers) is sequenced, how is it possible for the result to be 36 nt long? Am I looking at this way too simplistic or what?
Also: if I can align (bowtie2) enough reads to cover my entire virus sequence, how come after assembling (velvet) the contigs cover only fractions of the ref seq? How much of it is covered depends on number of reads mostly, kmer size a little also.
anything I can do to improve the assembly?
this is possibly a dumb question, but if my goal is to find siRNA (20-25 nt long) why are the Illumina reads 36 nt long, at least before quality trim? if a 24 nt long RNA piece (plus primers) is sequenced, how is it possible for the result to be 36 nt long? Am I looking at this way too simplistic or what?
Also: if I can align (bowtie2) enough reads to cover my entire virus sequence, how come after assembling (velvet) the contigs cover only fractions of the ref seq? How much of it is covered depends on number of reads mostly, kmer size a little also.
anything I can do to improve the assembly?
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