Question

recovery ribosomal 16S

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4.6 years ago

AbdelAbdel ▴ 30

how i can recover the 16S from a set of FASTA files. is there any script or utility that does that and thanks in advance

genome • 781 views

ADD COMMENT • link updated 4.6 years ago by h.mon 35k • written 4.6 years ago by AbdelAbdel ▴ 30

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What's your input? shotgun metagenomics? 16S amplicon?

ADD REPLY • link 4.6 years ago by Asaf 10k

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input : scaffold.fasta not metagenomicx yes for 16S

ADD REPLY • link 4.6 years ago by AbdelAbdel ▴ 30

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What did you assemble and how? You can annotate it with prokka and get the rRNA but the reliability depends on the assmebly

ADD REPLY • link 4.6 years ago by Asaf 10k

score 1 · Answer 1 · 2020-03-12

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4.6 years ago

h.mon 35k

Have a look at Barrnap and RNAmmer.

ADD COMMENT • link 4.6 years ago by h.mon 35k