importing read counts feature table

User Support
1

I have a table of read counts for each sample (I think it was generated using dada2) that I would like to import into qiime2 however none of the importable types seem to be appropriate. Here are the importable-types that seem to be appropriate for feature table:

FeatureTable[Composition]
FeatureTable[Frequency]
FeatureTable[PercentileNormalized]
FeatureTable[PresenceAbsence]
FeatureTable[RelativeFrequency]

Should I transform the data to relative frequency or frequency before importing? Also, should the data be tab separated or comma separated?

Here is an example of the data that I'm trying to import:

Taxa,S1,S2,S3,S4,S5,S6,S7,S8,S9,S10,S11,S12,S13,S14,S15,S16,S17,S18,S19,S20,S21,S22,S23,S24
T1,3644,45130,8919,78994,12342,116573,84437,51892,13806,83787,89021,124568,2134,43188,6851,22248,11926,54254,110651,342646,8958,52630,30440,76056
T2,31009,50431,9947,49646,3493,5188,6947,358,3273,17017,5007,3896,30314,121668,9049,60724,1409,1831,1707,164,2018,9153,2616,12258

Thanks!!
Mike

2

Hi @Michael_Thon,

This looks like a FeatureTable[Frequency], which is the format with raw counts. However, you may have to convert to a biom object, as suggested by the import tutorial.

Best,
Justine