As mentioned in the previous chapter, if you’d like to learn about this action, you could run the command qiime demux emp-paired -help, which will print help text to the screen. This action demultiplexes paired-end sequencing data that is formatted as is typical for Earth Microbiome Project (EMP) sequenced data (more on that later). The third space-separated component is emp-paired, which is an action in the q2-demux plugin. This is the name of the q2-demux plugin, as far as QIIME 2 is concerned, so this tells QIIME 2 that you want to use the q2-demux plugin. The second space-separated component is demux. This tells your computer that the QIIME 2 program should be run. The first space-separated component is qiime. There are four components to notice on the first line of this command, and as is typically the case when running command line software, the command’s components are separated by spaces.
#Demultiplex osculator software
As we look at this command, I’m going to assume that you either have some command line software experience, or that you’ve read the introductory chapter in this book on using the command line ( TODO: this chapter doesn’t exist yet.). Since this is one of the first QIIME 2 commands that you’ve run (at least while reading this book) let’s take a look at it in some detail. o - error - correction - details demux - log. m - barcodes - column barcode - sequence \ i - seqs emp - paired - end - sequences. These take the sequencing data as input, as well as the sample metadata. The q2-demux plugin in QIIME 2 has several methods for demultiplexing sequencing runs. Assign sequences to the sample they are derived from is referred to as demultiplexing the sequencing run. One piece of sample metadata in our sample metadata file is the barcode sequence associated with each sample. All sequences derived from sample-1 will have the sample-1 barcode associated with them, and all sequences derived from sample-2 will have the sample-2 barcode associated with them. For example, sample-1 might be assigned the barcode TGACCGTACGTA, and sample-2 might be assigned the barcode TGGTAGACCCGT. Instead, during sample preparation (PCR specifically), a short DNA sequence referred to as an index or a barcode was added to sequences on a per-sample basis. At this stage, the sequences are all grouped together - they are not grouped by sample. This is sequencing data as it came off an Illumina DNA sequencing instrument. The second file that we downloaded above was our multiplexed sequence data. This content will need to be contextualized for this chapter. I decided to simplify that chapter as much as possible. TODO: All content is currently copy/pasted from its previous home in the overview tutorial chapter.
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