Matrix-Count contains individual sequence reads as samples

[eme...@umich.edu]

Hello!
After I ran a set of samples through the mothur pipeline, my matrix-count table showed oligotypes per the individual sequence reads within each sample, not oligotypes by individual samples. What is causing this? How can I coerce mothur into collapsing the reads down by sample? Also, just so Im aware- what commands generates the Matrix-Count table?

Best,
E

[A. Murat Eren]

Your input FASTA file must be improperly formatted:

http://merenlab.org/2012/05/11/oligotyping-pipeline-explained/#preparing-the-fasta-file​

--

A. Murat Eren (meren)
http://merenlab.org :: twitter :: gpg

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[eme...@umich.edu]

Thank you! My fasta file is improperly formatted, is there an efficient way to reformat it? At what step does the formatting occur? Is it okay that my original data was in fastq format?

Thank you again for your help!

On Tuesday, August 29, 2017 at 2:45:47 PM UTC-4, A. Murat Eren wrote:

Your input FASTA file must be improperly formatted:

http://merenlab.org/2012/05/11/oligotyping-pipeline-explained/#preparing-the-fasta-file​

--

A. Murat Eren (meren)
http://merenlab.org :: twitter :: gpg

On Tue, Aug 29, 2017 at 1:38 PM, <eme...@umich.edu> wrote:

Hello!
After I ran a set of samples through the mothur pipeline, my matrix-count table showed oligotypes per the individual sequence reads within each sample, not oligotypes by individual samples. What is causing this? How can I coerce mothur into collapsing the reads down by sample? Also, just so Im aware- what commands generates the Matrix-Count table?

Best,
E

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To unsubscribe from this group and stop receiving emails from it, send an email to oligotyping...@googlegroups.com.

[A. Murat Eren]

The oligotyping pipeline does not have a specific tool to re-format a given FASTA file (it has a program to check whether it is properly formatted or not, though).

Best,

--

A. Murat Eren (meren)
http://merenlab.org :: twitter :: gpg

To unsubscribe from this group and stop receiving emails from it, send an email to oligotyping+unsubscribe@googlegroups.com.
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