comparative analysis of 16S rRNA sequencing data of different runs

[cherman2 (Chloe Herman)]

Hi @Harshita_Sharma,
Seems like you are doing really exciting research. Comparative analysis are tricky.

I am personally getting alittle lost in all your steps.

@Harshita_Sharma

i downloaded fastq.gz files from ncbi using SRA accession id and run FastQC which showed me presence of Illumina universal adapter in run 1 and 2 only which i removed using cutadapt. Then, i merged the paired end reads of run 1,2 and 3 followed by quality-filter q-score method for all the samples of 4 runs. then, i performed dereplication of all of these 4 run samples which gave me feature table and feature data as output. next, i proceeded with chimera removal using both denovo and reference based approaches, for which i got 3 output files [chimeric sequences, non-chimeric sequences and stats file].

Would you mind giving us a list of exact commands you ran? I think this might help our mods better understand what you are running and how to get you where you want to go!

@Harshita_Sharma

if i proceed with taxonomic annotation, how do i generate feature table for the above generated non-chimeric sequences?

I believe you need to filter your feature-table using the non-chimeric sequences like in this post: Error with vsearch uchime-denovo output - #8 by Oddant1

@Harshita_Sharma

this is what the stats file generated after chimera removal looks like:

Here is more info regarding the columns and what they mean: Galaxy |