My environmental sample was analyzed for fungi by both DGGE (18S) and NGS (ITS2), resulted in some different names (in the top 5 of strong bands in DGGE, or most abundant sequences in NGS) between the results of the two techniques.
My questions are:
1/ What possibilities could be for the different results?
2/ I want to know whether one species with the strong band in my DGGE could be one of "no blast hit" in NGS or not, so is there any way to discover this?
Thank you.
Some background reading would be this: Article Five simple guidelines for establishing basic authenticity a...
If the problem is, like you say "no blast hits", then try changing "Optimize for" to "Somewhat similar sequences (blastn)".
But I don't think a genuine fungal 18S (or ITS) sequence could ever result in "no blast hits". My guess is that the sequence is artificial - broken somehow. Use V-Xtractor (18S) and ITSx (ITS) to find out.
Did you quality filter, cluster, and taxonomically identify the sequences? Of course, 18S and ITS will target different fragment regions, and available reference sequences for these two markers differ. No blast hits mean some of your sequences have no reference in the database.
Hi Thakur
This reference is useful
I think that
Full-Length Multi-Barcoding: DNA Barcoding from Single Ingredient to Complex Mixtures
Article Full-Length Multi-Barcoding: DNA Barcoding from Single Ingre...
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