Good afternoon,
Please see at the end the different scripts I have implemented for trying to solve my problem, with # in ().
I am currently working with a bacterial 16S Illumina sequencing dataset.
I have cleaned, trimmed and assigned taxonomy (SILVA) using Mothur, following the whole pipeline.
I want now to use Tax4Fun (R package), instead of PICRUSt, to generate predictions of metagenome content.
To do so, I need a .biom file, which I have generated using the mothur function make.biom (1).
Now, I cannot import this .biom file in Tax4Fun for some reasons, although I have tried quite everything I could imagine : I always get the same error (2).
I contacted Tax4Fun authors, who have kindly sent me a sample QIIME-generated OTU_table.txt, so I could try and compare with mine. I converted my .biom file to .txt (3) to be able to compare. I didn’t notice any different (human-readable).
So I converted their .txt file to a .biom file (4) to try and see if I was properly using the import function of Tax4Fun and it worked (5). I tried to convert my .txt into a .biom file (6) to do the same and it did not work (7).
So my question is: is there something non-human readable in .biom files, that mothur and qiime would not write the same, that could lead to this different behaviour from Tax4Fun?
If so, and even if not, do you know any trick I could use to make it work?
Thank you very much in advance,
Cecile
(1) In mothur:
make.biom(my_shared.shared, constaxonomy=my_constax.0.03.cons.taxonomy)
Mothur answers:
0.03
Output File Names:
my_mothur_biom.biom
(2) In R:
importQIIMEBiomData ('my_mothur_biom.biom')
R answers:
Error in rowsum.default(as.matrix(taxProfile), ModSilvaIds) :
incorrect length for 'group'
(3) In Qiime:
biom convert -i my_mothur_biom.biom -o my_mothur_biom.txt --to-tsv
(4) In Qiime:
biom convert -i OTU_table_sample.txt -o OTU_table_sample.biom --to-hdf5 --table-type="OTU table" --process-obs-metadata taxonomy
(5) In R:
importQIIMEBiomData ('OTU_table_sample.biom')
(6) In Qiime:
biom convert -i my_mothur_biom.txt -o my_qiime_biom.biom --to-hdf5 --table-type="OTU table" --process-obs-metadata taxonomy
(7) In R:
importQIIMEBiomData ('my_qiime_biom.biom')
R answers:
Error in rowsum.default(as.matrix(taxProfile), ModSilvaIds) :
incorrect length for 'group'