Stripping Adapter Fragments
Taking data straight from a sequencing instrument in FASTQ format typically requires any remaining adapter fragments to be stripped from the data. To do this, use the Adapter Removal tool. A tutorial on how to use the Adapter Removal tool can be found here.
Filtering your Sequence Data
Occasionally, data that has had its adapters trimmed will require further filtering to remove sequences that are of no interest to the user. For example, stripping out T or R RNA sequences, removing sequences that do not match to the reference genome or removing sequences based on their length or abundance in the file (i.e. how many times the small RNA was sequenced during the experiment). To do this, use the Filter tool. A tutorial on how to use the Filter tool can be found here.
Aligning sRNA Data to a long read file such as a Genome
Certain tools within the workbench require an aligned sequence file (such as VisSR) or you may wish to align sequences for another type of analysis. To do this use the Sequence Alignment tool. A tutorial on how to use the Sequence Alignment tool can be found here.