Difference between revisions of "Template:Group by titles 2D"
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This function is typically used to create "OTU Table" from sequences that have been clustered and contain the unique sample name(number) and unique cluster name(number) in the sequence title. (See [[FASTA form#Edit titles (replace, change, resize)|Edit titles]], [[FASTA form#Group by titles|Group by titles]] and [[FASTA form#Complete-link clustering or UPARSE (USEARCH)|clustering]] functions for details how to modify titles and cluster sequences.)<br> | This function is typically used to create "OTU Table" from sequences that have been clustered and contain the unique sample name(number) and unique cluster name(number) in the sequence title. (See [[FASTA form#Edit titles (replace, change, resize)|Edit titles]], [[FASTA form#Group by titles|Group by titles]] and [[FASTA form#Complete-link clustering or UPARSE (USEARCH)|clustering]] functions for details how to modify titles and cluster sequences.)<br> | ||
| − | First you group your sequences by sample name(number) on the FASTA form. This grouping takes you to Grid form (listing number of sequences in each sample). Now (on the Grid form) you choose option - Group by titles 2D - in the Divided dataset menu and set the parameters to group by the cluster name(number). A 2D tab delimited table will be created that | + | First you group your sequences by sample name(number) on the FASTA form via the Group by title option in Title menu. This grouping takes you to Grid form (listing number of sequences in each sample). Now (on the Grid form) you choose option - Group by titles 2D - in the Divided dataset menu and set the parameters to group by the cluster name(number). A 2D tab delimited table will be created that lists how many sequences of each cluster is contained within each sample. Copy and paste or save file to a desired location <br> |
Revision as of 11:57, 15 July 2015
Group by titles 2D
This function is typically used to create "OTU Table" from sequences that have been clustered and contain the unique sample name(number) and unique cluster name(number) in the sequence title. (See Edit titles, Group by titles and clustering functions for details how to modify titles and cluster sequences.)
First you group your sequences by sample name(number) on the FASTA form via the Group by title option in Title menu. This grouping takes you to Grid form (listing number of sequences in each sample). Now (on the Grid form) you choose option - Group by titles 2D - in the Divided dataset menu and set the parameters to group by the cluster name(number). A 2D tab delimited table will be created that lists how many sequences of each cluster is contained within each sample. Copy and paste or save file to a desired location
