Question: Where can I find B cell isotype information for the annotated contigs?
Answer: B cell isotype information can be obtained from various output files generated by the cellranger vdj pipeline.
1) From the all_contig_annotations.csv file: The "c_gene" column identifies the C gene assigned to any given contig. The C gene can identify the isotype of the contig. This file is described in detail here.
2) The .vloupe file: follow these steps to find isotype information in the .vloupe file.
- Open the .vloupe file in the Loupe V(D)J Browser.
- There are two additional summary charts that allow you to analyze the isotype distribution. To access these, return to the chart view by clicking the bar chart icon. Then click the Chart Type dropdown and scroll to the bottom of the list to find the B-Cell Isotypes and B-Cell Paired Isotypes charts.
- First, select the B-Cell Isotype chart. This chart displays the frequency of immunoglobin isotypes and the type of light chains in the sample.
- Next, select the B-Cell Paired Isotype chart. The chart displays the distribution of paired isotypes and light chains among clonotypes in the sample. Only clonotypes where there is exactly one heavy chain and one light chain are included in this chart.
For more information on working with B cell data in Loupe V(D)J Browser, please see the Loupe V(D)J Browser Tutorial: B Cells.