Question: I am trying to get the B Cell isotype information for the annotated contigs, where can I find this information?
Answer: B cell isotype information can be obtained from various output files generated by "cellranger vdj" pipeline.
1) From all_contig_annotations.csv file. This file is described in detail here. One of the columns in this file "c_gene" identify the C gene assigned for a given contig. The C gene in this column can identify the isotype of the contig.
2) You can also get this information interactively by opening the .vloupe file in Loupe V(D)J Browser.
When viewing a B cell sample, there are two additional summary charts which 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 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.