Hello there, I run 16S RNA analyses with Qiime. I am facing an issue in the final step. I run the analyses of two distinct batches of samples and then I merged the OTUs tables. I found out a huge loss of information in terms of the number of OTUs and the number of sequences per sample compared to the OTU table from each distinct run. I tried then to merge the sequences (cat seqs.fna, seqs.fna> merged.fna) and the mapping files after demultiplexing and run the whole downstream analyses. I gained the same results of merging the OTU tables at the end of the two individual runs.
Does anybody know what is due to this loss of information and how to avoid this?
thanks, everybody for your kind attention and help!
•
written
by
chiara.conte91 •
1 answer
Hello Chiara,
How did you exactly use the feature-table merge command ?
It makes sense to have "less" OTUs after merging, as some OTUs may be shared by the two tables. You should have as many OTUs as the union of OTUs from run 1 and OTUs from run 2. However, as far as I know, it should not impact the number of reads per sample. Erwann
Log in to answer this question.
-
ERROR RAISED DURING STEP: Assign taxonomy
written by pasha64t •
-
OTUs table is almost totally different for the same batch sample with different sequencing batches
written by Mengying •
-
How to split fastq file contains two different header information
written by goh •
-
16S rRNA de novo otu picking analysis
written by dcron13 •
-
Convert biom to tabular file and parse taxonomic levels
written by naphtali.paul •
-
16S sequencing analysis: from fasta to otu to PCA&Heatmap
written by shlomsauce •
-
USEARCH in small batches?
written by Ronald Rodriguez •
-
Best way to generate rarefaction curves from 16S/18S data-reclustering?
written by ben83 •
-
Best strategy for matching OTU sequences from different runs?
written by rodrigues.pap •
-
Diversity Analysis From 454 Data (No 16S Amplicons)
written by Iddo
