| OBISTAT(1) | OBITools | OBISTAT(1) |
obistat - description of obistat
obistats computes basic statistics for attribute values of sequence records. The sequence records can be categorized or not using one or several -c options. By default, only the number of sequence records and the total count are computed for each category. Additional statistics can be computed for attribute values in each category, like:
The result is a contingency table with the different categories in rows, and the computed statistics in columns.
TIP:
Example:
> obistat -c sample -c seq_length seq.fasta
This command prints the number of sequence records and total count for each combination of sample and sequence length.
Example:
> obistat -c sample -m seq_length seq.fastq
This command computes the minimum sequence length observed for each sample.
Example:
> obistat -c sample -M seq_length seq.fastq
This command computes the maximum sequence length observed for each sample.
Example:
> obistat -c sample -a seq_length seq.fastq
This command computes the mean sequence length observed for each sample.
Example:
> obistat -c genus_name -v reverse_error seq.fastq
This command computes the variance of the number of errors observed in the reverse primer for each genus.
Example:
> obistat -c genus_name -s reverse_error seq.fastq
This command computes the standard deviation of the number of errors observed in the reverse primer for each genus.
The OBITools Development Team - LECA
2019 - 2015, OBITool Development Team
| January 28, 2019 | 1.02 12 |