Dear community,
Currently I'm obtaining mitogenomes of several species through de novo assembly using Novoplasty. In many samples and regardless the seed I use I obtain in some positions an asterisk (*) instead a nucleotide. I'm interpreting that as an ambiguous nucleotide (N?), but I'm not sure if I'm right. I'm not able to find what means that. Anyone knows for sure?
Best regards,
Fernando.
I have never used Novoplasty, but I might have one idea to test if the asterisk represents an ambiguous nucleotide or a coverage drop: you could map your reads back to your assembled organelle, and check the % of each nucleotide in that particular position. It won't solve your Novoplasty issue, but at least you would now what is going on there.
Thanks Samuel Abalde! I try both deleting the asterisks and substituting them with N, and submitted both options for annotation in MITOS2. I found out that if you just delete them, the gene lose the nucleotide and the reading pattern altered. Novoplasty account for other IUPAC ambiguity codes as far as I can see, so I'm pretty sure it is a synonym of N.
Yes, I do think your guess is right. Have you checked the presence of "*" or ambiguous nucleotide in your input sequences? Samuel Abalde
Thanks Sunil Kumar Sahu for your answer. I just checked in my FASTQ files. Asterisks are not included. As far as I understand, they usually do not designate a nucleotide in Illumina, but I might be wrong on that. However, there are a few Ns with low shred values, so they must have been deleted by the Novoplasty algorithm during the assembly.
Looking at the script of Novoplasty: https://raw.githubusercontent.com/ndierckx/NOVOPlasty/master/NOVOPlasty3.8.3.pl
And searching for: =“*”
It seems the program put * in deletion or a potential “start codon”?
Sorry I am not into perl too much, perhaps asking a collegue with expertise in perl and showing the code can help.
In any case, mapping your reads back to that fragment (and view it with samtools tview) can help to figure out what those * are.
No problem Fernando Ángel Fernández-Álvarez . I found this today :https://github.com/ndierckx/NOVOPlasty/wiki/Interpretation-&-post-processing
Hope it helps!
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