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transcript / samsa2

SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customizable reference databases.
GNU General Public License v3.0
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SAMS2 bash script for 16S rRNA pipeline #44

Open Shicheng-Guo opened 4 years ago

Shicheng-Guo commented 4 years ago

Dear Sam,

I think it will be great if you can provide a bash script for 16S rRNA pipeline. what we need to do is replace the 16S rRNA from SortMeRNA to the following steps, rather than reads of non-16S rRNA.

Thanks.

Shicheng

transcript commented 4 years ago

This should be feasible, although keep in mind that the results would only really be useful for organism identification (since there's not going to be any functional information derived from the 16S sequences).

It also may require a different reference, since it would be better to annotate against GreenGenes or SILVA instead of just RefSeq overall...