Dear all,
I would like to know how can I remove the sequences of 16S rRNA gene from chloroplast that were identified in QIIME and Greengenes?
I created the OTUs and the did the pipeline up to the identification. However, in the phylogenetic identifications some are from chloroplasts and I want to remove them before submission to NCBI.
Could you please help me with this?
Thank you very much in advance.
Diogo Proença
You could either filter out the chloroplasts with filter_otus_from_otu_table.py or you could delet them manually from the excel table after you did the biom_convert step (biom convert –i otu_table.biom –o folder/biom_excel.txt –b -–header-key taxonomy) and also maybe after you checked those sequences like Miguel suggested.
http://qiime.org/scripts/filter_otus_from_otu_table.html
Use the -e option with an input of the sequence headers you want to filter out of your otu table.
Some of your 'chloroplast' sequences might correspond to cyanobacterial organisms. This is especially frequent when using RDP more than Greengenes. However, I would recomend you to create a .fasta file with all your potential chloroplastic sequences to further search for taxonomic identities in GenBank. This proccess won't be difficult and your results will be more reliable.
Good Luck
You could either filter out the chloroplasts with filter_otus_from_otu_table.py or you could delet them manually from the excel table after you did the biom_convert step (biom convert –i otu_table.biom –o folder/biom_excel.txt –b -–header-key taxonomy) and also maybe after you checked those sequences like Miguel suggested.
Convert it to txt as suggested above and then run:
grep -iv "chloroplast" OtuTable.txt > OtuTable_filtered.txt
The verbose option "-v" will skip every line containing "chloroplast" in upper or lower case (the "-i" option).
Convert it back to biom.
I've done something similar by using the filter_taxa_from_otu_table.py command in qiime.
filter_taxa_from_otu_table.py -i file.biom -n c__Chloroplast -o nochloroplast.biom
I've also used this command to take out sequences to check the taxonomy. For this I use -p instead of -n to keep just have the sequences I'm considering removing and then biom filter the fasta file:
filter_fasta.py -f initial_repset.fna -b chloroplast.biom -o chloroplast_repset.fna
You should have a fasta file of just the chloroplast sequences and can check them with BLAST and/or phylogenetic analysis.
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