# Dealing with samples with low read counts

**URL:** <https://forum.mothur.org/t/dealing-with-samples-with-low-read-counts/3027>\
**Category:** Journal club\
**Created:** [October 20, 2016, 1:09pm UTC](https://forum.mothur.org/t/dealing-with-samples-with-low-read-counts/3027 "2016-10-20T13:09:27Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Dr\_Nezar](https://avatars.discourse-cdn.com/v4/letter/d/ebca7d/32.png) [@Dr\_Nezar](https://forum.mothur.org/u/Dr_Nezar)\
**Post date:** [October 20, 2016, 1:09pm UTC](https://forum.mothur.org/t/dealing-with-samples-with-low-read-counts/3027/1 "2016-10-20T13:09:27Z")

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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

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**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\
**Post date:** [November 1, 2016, 5:55pm UTC](https://forum.mothur.org/t/dealing-with-samples-with-low-read-counts/3027/2 "2016-11-01T17:55:21Z")

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You either rarefy to the smallest sample, resequence those samples, or you exclude them. Remember that not too long ago, people were doing awesome science with less than 100 sequences.