There was a problem this morning that caused some reads to be double counted in the table. This has now been fixed; the abundance numbers for this dataset now match the number of sequences they represent. Thank you for alerting us to the problem. William Trimble for the MG-RAST team On Mon, Jun 27, 2011 at 8:39 AM, Peter Ahrens <[email protected]> wrote:

The dataset is my own 22-hel (4466709.3 if you have access to that) and the "abundance number is the sum of the abundance of all the species and the unassigned. I just wondered whether more hits than sequences could indicate that some of the sequences hit more than one species? And if so, would a chimera give rise to more hits when using short alignement length but only one (or zero) when using a longer  alignment length?

Peter

-----Oprindelig meddelelse----- Fra: William Trimble [mailto:[email protected]] Sendt: 27. juni 2011 15:02 Til: [email protected]; Peter Ahrens Emne: Re: [mg-rast] Hits and minimum length

Thanks for using MG-RAST.

The similarity searching step in MG-RAST isn't specifically designed to identify chimeras.  It performs a similarity search and allows you to filter the results of the search.  It could be chimerism, but it could just be that the best database hits don't align particularly well.

On the face of it, it makes sense that more stringent filters will yield fewer species and fewer hits.

I haven't been able to reproduce the numbers you report below -- which dataset are you using, and which annotation source (RDP, greengenes, or SSU)?  Where are you taking the "abundance" number from?

William Trimble for the MG-RAST team

On Mon, Jun 27, 2011 at 2:00 AM, Peter Ahrens <[email protected]> wrote:

...

I am examining a sample of 8150 16S sequences to the species level. When I change  the minimum alignment length cut off, the results changes dramatically:

LENGTH / SPECIES / TOTAL NUMBER OF HITS

150 / 23 / 13576

200 / 21 / 13537

250 / 19 / 11907

275 / 14 / 6245

300 / 14 / 5097

The average length of my sequences is approximately 400 bases.

Does the high number of hits with the 150 setting indicate chimeras? Or why will 8150 sequences give a total of 13576 hits?

Thanks in advance

Peter

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Peter Ahrens

STI Research

AMOF

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Statens Serum Institut

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Copenhagen

Denmark

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