Dear all,
I have recently started using the cellranger from 10x for scRNA-seq data, after having used my own pipeline (with STAR alignment) for smart-seq2 data, to get the count matrix for then later analyzing with Seurat or Scanpy.
I have however faced a strange issue: not all genes appear in the features.csv file. For example, the gene Clec7a does not appear, which seems strange to me. I then checked the total number of features present in the features.csv file and it was approximately 32000, which is very different from the 53000 I used to have with my own pipeline. This seems to indicate that the genome annotation files (gtf) are somehow different.
Does 10x filter the genome annotation file in a certain way to decrease the number of genes? Is there an option to control this?
Note: I use the same reference genome version in my own pipeline as the 10x one.
1 answer
I assume you are talking about mouse
Here's the entry for that gene in the gtf I downloaded from ensembl
6 ensembl_havana gene 129438554 129449742 . - .gene_id "ENSMUSG00000079293"; gene_version "12"; gene_name "Clec7a"; gene_source "ensembl_havana"; gene_biotype "polymorphic_pseudogene";
See also the ensembl entry: Look at the "gene type" in the summary
If you filter the gtf the way 10xGenomics suggest, that's going to be filtered away. I don't know why the gene is so labeled, when it has transcripts which are counted as protein coding.
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