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High read abundance but no bins #211
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Hi Zahid,
How many samples do you have? Have you done any taxonomic annotation of
contigs to figure out where the protoebacterial data endend up? If they are
not in any bins they must be in contigs shorter than the cutoff for
binning. The reason for this can be either low coverage of high
intra-population diversity. If you do have proteobacterial contigs in
impure bins or highly incomplete bins the reason can probably be too low
number of samples.
Kind regards,
Anders
…On Thu, Sep 27, 2018 at 10:35 AM zahidrehman ***@***.***> wrote:
Dear, I have metagenome assembly of two samples that I am trying to bin.
Although I have a high abundance of Proteobacterial reads, after binning I
don't get any Proteobacterial bin. What could be the possible reasons?
Coverage should not be an issue; since I have high read abundance. I don't
expect too much strain variation since these are biofilm samples. I know
CONCOCT struggles with binning if samples are too few. However, I do get
bins for other bacteria whose relative abundance of reads is less than
Proteobacteria. Any comments would be highly appreciated.
Best Regards
Zahid
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Dear Andres, |
Hi again @zahidrehman, Best, |
Dear, I have metagenome assembly of two samples that I am trying to bin. Although I have a high abundance of Proteobacterial reads, after binning I don't get any Proteobacterial bin. What could be the possible reasons? Coverage should not be an issue; since I have high read abundance. I don't expect too much strain variation since these are biofilm samples. I know CONCOCT struggles with binning if samples are too few. However, I do get bins for other bacteria whose relative abundance of reads is less than Proteobacteria. Any comments would be highly appreciated.
Best Regards
Zahid
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