Hi, everyone,
I sequenced some samples in the Illumina MiSeq, got the results but now I don't know how to analyze them. I already read the User guide from Illumina, but it's only about the Analysis Viewer. Do I need to import the data to another software or is there one specific from Illumina that may organize the data in a better way?
Thanks in advance!
Adriana Cravo Can you please elaborate your question regarding what amplicon you sequences on MiSeq.
Nevertheless, if you have used any sequencing facility for their service, you might have got ready made data which you need to process in your data analysis pipeline. Nevertheless, there are many good tutorials for this purpose. Please have a look on DADA2, QIIME2 and mothur pipelines on google. There are several papers and workflows available which you can refer too.
Dear Adriana, as you can see, currently there are diverse pipelines to deal with high-throughput sequencing data. Here is some tips, hoping useful for you.
1. I strongly recommend you to read as many papers as possible. You can find detailed methods and pipelines in diverse papers. It is always best to learn to find answers by yourself.
2. Although DADA2 and QIIME, or Mothur is useful, I don't think they are easy to access for beginners. I suggest USEARCH or the online GALAXY. These two ones are easy to understand and interface-friendly.
3. It is not easy to start. The key point is trying to understand the whole analysis as an integrity.
Best wishes.
Yuzhan
Dear Adriana,
Illumina provides the MiSeq Reporter that can be used to align reads and do variant calling. Alternatively you can perform analysis yourself, for instance using BWA-MEM for alignment and GATK HaplotypeCaller for variant calling.
Regards,
Lennart
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