Hi,
What is the best approach to deal with samples that end up, after removal of chimeras and irrelevant lineages, with low read counts. See the following set for example:
Sampleid final read count
C1 2517
C2 17816
C3 14658
C4 11124
C5 31872
C6 57057
C7 2808
C8 54960
C9 11080
C10 27527
C11 4381
C12 17940
C13 27194
C14 31440
C15 37722
C16 41290
C17 33316
C18 50601
C19 25910
C20 14893
C21 21733
C22 7178
C23 5423
C24 21945
C25 1359
C26 37299
C27 45890
N1 9614
N2 28719
N3 17400
N4 23787
N5 11208
N6 20586
N7 7749
N8 16744
N9 13535
N10 3282
N11 15922
N12 9362
N13 12161
N14 22725
N15 10406
N16 30364
N17 21540
N18 12046
N19 9102
N20 7413
N21 19050
N22 417978
N23 37831
N24 48710
N25 13707
N26 21922
N27 41508
N28 11752
Median 17940
Subsampling according to the sample with lowest count will result in significant loss of reads from the other samples and will negatively impact on richness and diversity estimates. Any advice?
Regards
Nezar Al-Hebshi
Kornberg School of Dentistry
Temple University