Fixed Length Trimming
The Fixed Length Trimming tool has been moved to Legacy Tools folder because the OTU Clustering tool can now deal with reads with variable lengths. The input sequences are aligned to reference OTU sequences (e.g. the reference database) and, if the input sequence is shorter, the unaligned ends of the reference are ignored.
In previous versions of the software, in order to compare sequences and cluster them, they all needed to be of exact same length. All reads which are shorter than the cut-off were discarded, and reads longer than that were trimmed back to the chosen length.
In order to compare sequences and cluster them, they all need to be of exact same length. All reads which are shorter than the cut-off are discarded, and reads longer than that are trimmed back to the chosen length.
To run the tool, go to
Microbial Genomics Module (
) | Metagenomics (
) | Amplicon-based OTU clustering (
) | Fixed Length Trimming (
)
and select the sequences you would like to trim.
In the next wizard window you can enter manually the desired length for the trimmed reads. Alternatively, the Fixed length Trimming algorithm can calculate the trimming cut-off value as the mean length of the merged reads minus one standard deviation. If this option is chosen, it is important that all samples are trimmed at the same time as the mean and standard deviation for the combined reads in all samples needs to be estimated at once.
You can also offset one adapter or barcode by typing the nucleotide sequence in the Primer offset window. Exact matching is performed but ambiguous symbols are allowed. For more than one adapter, we recommend to perform prior to the Fixed Length trimming a Trim Sequences step from the NGS Core Tools in which you can import an adapter list (see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Adapter_trimming.html).