What is Trim tags?

The Trim tags task allows you to process unaligned read data with adaptors, barcodes, and UMIs using a Prep kit file that specifies the cofiguration configuration of these elements in your NGS reads. 

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• Click an Unaligned reads data node
• Click the Pre-alignment QA/QC section of the toolbox
• Click Trim tags

There are two three parameters to configure - Prep kitand, Keep untrimmed, and Map feature barcodes.

Selecting Keep untrimmed will generate a separate unaligned reads data node with any reads that do not match the structure specified by the prep kit.  This option is off by default, to save on disk space. Selecting Map feature barcodes is only necessary for processing protein data from 10x Genomics' Feature Barcoding assay (v3+ chemistry). For single cell gene expression data, leave this option unchecked.

Partek distributes prep kits for processing several types of data:

• Drop-seq
• 10x Chromium Single Cell 3' v2
• 10x Chromium Single Cell 3' v3
• 10x Chromium Single Cell 5'
• Drop-seq
• Lexogen QuantSeq FWD-UMI
• Bio-Rad SureCell WTA 3'
• Fluidigm C1 mRNA Seq HT IFC
• Rubicon Genomics ThruPLEX Tag-seq
• 1CellBio inDrop

If your data is from one of these sources, you can select the appropriate option in the Prep kit drop-down menu. If the data is from another source, you can build a custom prep kit file to process your data.

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The output of Trim tags is a Trimmed reads data node. An additional Untrimmed reads data node will be generated if the Keep untrimmed option was selected.

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Like adaptors, barcodes can be specified using a file or manually specified, but you can also choose to designate any a segment of arbitrary length in the sequence as the barcode. This is useful if you do not have a specific set of known barcodes. 

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