Hi,
As a beginner to Microbiome data analysis using QIIME 2, how can I know whether the SRA files that I have downloaded in fastq format is demultiplexed or not?
If not demultiplexed how can I get the barcode sequence from those SRA files if not provided for demultiplexing step in QIIME2?
How can I perform a data analysis [ SRR6330729 ] on these data set provided in NCBI without the information on the sample metadata file and the barcode sequences?
Thankyou
Is this post a General Discussion topic? Have you reviewed the QIIME 2 Forum Glossary? Post to this category if you have a general question about microbiome science, bioinformatics, or other general questions, ideas, or topics to discuss. Please do not post questions here that have to do with technical support requests. Posts in this category are not guaranteed a response.
One of the easiest ways to see if your data is demultiplexed is to ask the providers of your samples. An easier method is to check how many files you have in general. Demultiplexing separates one large sequence into its individual samples based on given barcodes. Thus if you were given one large SRA file, it's safe to expect that this is multiplexed. If you sent in several sequences and got back the same number of files, it might be safe to call this demultiplexed. would you mind sending a screenshot of the files in their original naming format also?
I have taken the dataset with SRA accession number 6330729. I have sent the screen shot of an SRA file that has been downloaded in fastq format. Also I have sent the screenshot of the file opened.
I guess this is multiplexed? I want to know whether barcode sequences are required for analysis through QIIME2? If barcode sequences are required for analysis through QIIME2, apart from asking the barcode sequence from the real authors, is there any way to get the barcode sequences from these SRA files working on a command line interface?
I hope you got my point, sorry if the question is too basic. I am new to this platform of microbiome analysis through QIIME2. I am a Post graduate student in Bioinformatics and as a part of my academic project, I have chosen to work on QIIME2.
It would kind enough if you can suggest on how can I start learning this tool, since some terms are confusing. Is it enough to start with the moving tutorials examples to learn about QIIME2? or as a beginner is there anything to learn before working on the examples.
I guess this is multiplexed? I want to know whether barcode sequences are required for analysis through QIIME2? If barcode sequences are required for analysis through QIIME2, apart from asking the barcode sequence from the real authors, is there any way to get the barcode sequences from these SRA files working on a command line interface?
These are probably multiplexed. One clue is that the read lengths are ~160, showing that barcodes haven't been removed yet. Yes, you would need to know the barcodes used by these researchers to move forward, and people are not always good about uploading these as metadata to databases. You can also tell that something strange is going on with the quality scores.
As you mentioned, it will be a far better and less frustrating learning experience to follow one of the qiime tutorials, which come with curated data.
You can simply install the q2-fondue plugin and let it do all the work of preparing :qiime2: formatted data for you.
Generally speaking, all amplicon data in the SRA should already be demultiplexed, as it is required that data be demultiplexed for upload to the SRA. The SRR/SRX/SAMN files usually contain sequence data from a single sample. If you'd like to download a bunch of samples from a given study, then you'll want to access via the BioProject ID or a list of SRRs.
