There are some cases where .txt file format is needed to export and import donor and recipient genotypes into ChimerMarker instead of using the original pre-sample .fsa files. Sometimes when the donor and recipient .fsa files are from different CE machines, this can result in a large PCR migration shift between the two files. Other times a migration shift can occur with cases being tracked over a long time period. Eventually, the post-samples will no longer fall into bin with the donor and recipient profiles in their chimer panel. In these scenarios, we can take already genotyped recipient and donor profiles and turn them into a text file to be used with post-samples exhibiting a migration shift.
Instructions for making the text file from the ChimerMarker allele table, editing the file into the correct format, and importing the properly formatted text file into a new ChimerMarker project with the post-samples are below:
Exporting the allelic table text file:
- Go to View -> Preferences -> Chimerism tab and deselect “Show Ladder Samples in Report” and “Show Control Samples in Report”
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Click OK to apply preferences.
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Click the drop-down on the dye selector and select “Show All” to display all dye channels
- Click the Report Setting icon (A) above the allele table and select Chimerism for Report Style and Horizontal for Orientation.
- Deselect “Extend Diploid Homozygous” Option and click OK to apply.
- Click brown disk icon (B) to Save Report to File
- Name file and select Save as type: Text File (.txt)
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Click Save and then navigate to location the .txt file was saved to.
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The text file can be Opened With Excel or Notepad to perform edits, but must be resaved as a .txt, not as a .xls
Note: Editing in Excel may be easier than in NotePad.
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Delete all rows above Markers and any rows containing post samples.
- Delete columns before Donor1 and Recipient sample names.
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Rename Donor and Recipient, if needed to be exactly Recipient, Donor1 (and Donor2, if double-donor is present) for the software to properly identify.
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Each Marker must have two columns. Delete any extra columns in between markers.
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If a marker is homozygous for both donor and recipient than insert a blank column to ensure that there are two columns for that marker.
Showing proper table format below for donor and recipient profiles for single (top) and double (bottom) donor data.
Page 17 of the ChimerMarker_UserManual_v3.1.8 covers Creating the Text File Using Excel and Importing Text File into ChimerMarker
Text File Format Requirements:
-This excel file must be formatted as shown above and saved as .txt tab delimited file
-Donor1 (and Donor2, if applicable) and Recipient in first column
-There must be two columns for each marker (even if they are homozygous), which will sometimes require to insert empty columns to get the needed format (such as with DYS marker or in a marker where both individuals are homozygous)
-Do not use the extended homozygous table setting when creating allele table for this use
Importing the text file into Run Wizard during the chimerism (chimer panel creation) step:
- To import text file, go to the Data Process window of Run Wizard
- From the Allele Call section select option Please Enter Grouping File Path, then click folder icon
- Click Import and navigate to the Donor/Recipient text file and Open
- Check that the table looks accurate
- Select Label from Data type of auto create CHM Panel then click OK
- The file path for the text file should now appear in the run wizard.
Text file import format for single-donor case:
Text file import format for double-donor case: