High proportion of na ??

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High proportion of na ??

Post by ptranvan on Fri Jun 24, 2016 1:16 pm

Hi,

Based on that figure:



1) It seems that I have a lot of na. Why and is there a way to reduce that proportion ? (i've tried 0.1 and 0.25 coverage: same results)

2) These NAs are unnannotated TEs or it can be single dna (not TE) ?

3) Where is the file from which this figure is plotted ? (If I want to make my own plot).

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Re: High proportion of na ??

Post by Clément Goubert on Mon Jun 27, 2016 6:33 pm

Hi Patrick,

First of all, I am terribly sorry I didn't saw your last post on the forum, I usually have automatic emails bur for an unknown reason I wasn't notified. I am really sorry for the delay.

To answer your questions: the high proportion of na is indeed really intriguing. However, there could be several (and non-exclusive reasons for that).
1) you may have microbial contamination of your reads, that could leads to a high proportion of na. A good way to be sure of that would be first to blat your na contigs against nt.
2) Depending of the genome size of your species, as well as the level of ploidy, 0.1X or 0.25X may be already a high coverage thus you assemble some non or low repeated regions (multigenic families?)
3) Some of the na can also be unknown TEs, it would be interesting to study and manually try the annotation of the most abundant non-annotated na contigs

Finally, the data to build the graph are in the file Counts.txt of your output folder, it is for each class the total number of bp that align the database.
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