Hi. I tired to get taxonomic information of LSU fungal community using “qiime feature-classifier classify-sklearn”. I got the database from SILVA, release 119. I trained the database by using this tutorial ( Training feature classifiers with q2-feature-classifier — QIIME 2 2018.6.0 documentation ).…

Hi @F18D029G , It looks like your barplot did not attach — could you please try again? It may be too large to upload here — you may need to produce a smaller example barplot (filter out samples first), or post to dropbox etc and share the link here. [image] F18D029G: most sequences were not ass…

out of interest, what orientation tool pre-qiime2 import would you recommend for mixed orientation reads?

[image] mouldinator: out of interest, what orientation tool pre-qiime2 import would you recommend for mixed orientation reads? See this topic .

[LSU] Sorry, I missed upload. Can you see my barplot?

Thanks for uploading! I am guessing that this is a level 2 view and e.g., Dikarya are classified more deeply. Since you say those unclassified sequences BLAST to known species, I suspect this may be a mixed read orientation issue. You can try re-orienting reads, or use one of QIIME 2's other taxono…

I tried feature-classifier classify-consensus-blast. I got simillar result, so I have issue about my reference. [LSU_BLAST] I used SILVA119 database for qiime. ( https://drive.google.com/drive/folders/0Bz1utnb_nbhIfmFJRWxJeFdMOEk2emVBbWxxNy1LZVVBRllkeVdXbWtvMVJIZDdKYjNPV3c ) Does anyone who is a…

Hi @F18D029G , Indeed, looks like this is probably an issue with the reference. What steps did you take to format the reference sequences and taxonomy? I imagine SILVA is fine for LSU analysis but I am not sure. RDP also has a fungal LSU database that you could download for this. I have not used e…

Hi I used command this site. ( Training feature classifiers with q2-feature-classifier — QIIME 2 2018.8.0 documentation ) I tried finding RDP fungal LSU database, but I couldn't find. I want to know method of download RDP fungal LSU database. I use fungal specific primer. So, my sequence data is…

[image] Nicholas_Bokulich: What steps did you take to format the reference sequences and taxonomy? What I meant is: did you just download the SILVA LSU database and import to QIIME 2 or did you take any other steps to format those files? Could you send me the fasta and taxonomy file that you …

Hi I got SILVA119 database for qiime. ( https://drive.google.com/drive/folders/0Bz1utnb_nbhIfmFJRWxJeFdMOEk2emVBbWxxNy1LZVVBRllkeVdXbWtvMVJIZDdKYjNPV3c ) I used command upload txt. txt.txt (2.1 KB) I tried NCBI blast search Unassigned sequence. I got Camptobasidium, Lactifluus,Uncultured Glomero…

Analysis of fungi at LSU (28S)

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Nicholas_Bokulich (Nicholas Bokulich) October 16, 2018, 1:41pm 6

See this topic.