I have extracted DNA from cows milk using Promega FFS Nucleic Acid extraction kits and Promega blood cell DNA purification kits in Maxwell 16 automated system. Now after quantification and bio-analysis, I performed NGS following library preparation using Illumina Nextera XT library preparation kits (NextSeq 500 machine) with a concentration of 0.2ng DNA per micro-liter, and got the sequence result. After QC and downstream analyses, I found only 0.122 million mapped reads/sample, which is too low for a typical microbiome study. I need at least 4.0 - 6.0 million mapped reads/sample from the DNA samples. What can I do now? or Shall I go for further DNA concentration? If so, how I can concentrate the DNA samples?
We can help with using Galaxy at this forum. For community advice about tuning laboratory methods, try a general biology/bioinformatics forum. Examples: https://www.biostars.org, http://seqanswers.com, and https://stackoverflow.com.
I am not sure if you are doing the analysis in Galaxy or not, but a data format or tool usage issue can also lead to unexpected results (when using any bioinformatics tools, in Galaxy or not). So you may want to also review here if using Galaxy for those steps:
- Galaxy tutorials, including those for metagenomics: https://galaxyproject.org/learn/
- Galaxy FAQs: https://galaxyproject.org/support/
Thanks, Jen, Galaxy team