using gene_id rather than gene_name when reading in 10X data

[andyrussell]

When using the 'Read10X' command, Seurat reads in the genes.tsv file (from the CellRanger output) and reads in the gene_name (second column in the genes.tsv file) to your Seurat object e.g. genes.tsv file:

$ head filtered_gene_bc_matrices/hg19/genes.tsv
ENSG00000243485    MIR1302-10
ENSG00000237613    FAM138A
ENSG00000186092    OR4F5
ENSG00000238009    RP11-34P13.7
ENSG00000239945    RP11-34P13.8
ENSG00000237683    AL627309.1
ENSG00000239906    RP11-34P13.14
ENSG00000241599    RP11-34P13.9
ENSG00000228463    AP006222.2
ENSG00000237094    RP4-669L17.10

(source: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices)

This is obviously the most useful option for well annotated organisms such as mouse and human (as it's easier to work with shorter, distinct gene names) but in my case, many of the gene names are the same and I was wondering if there was a way to read in gene_ids instead (i.e. the 1st column in the genes.tsv file from the CellRanger output), and if not, if this could be an option in 'Read10X'?

Failing this, would anyone have any advice on how to possibly manipulate the genes.tsv file post CellRanger output to allow me to read in a modified genes.tsv file?

Thank you for any help you can give in advance!

[ChristophH]

In the develop branch, I've added an option gene.column to the Read10X function. The default value is 2 for gene names, but in your case setting it to 1 should give you the gene IDs.

…

On Thu, Jul 19, 2018 at 1:51 PM Andy Russell ***@***.***> wrote: When using the 'Read10X' command, Seurat reads in the genes.tsv file (from the CellRanger output) and reads in the gene_name (second column in the genes.tsv file) to your Seurat object e.g. genes.tsv file: $ head filtered_gene_bc_matrices/hg19/genes.tsv ENSG00000243485 MIR1302-10 ENSG00000237613 FAM138A ENSG00000186092 OR4F5 ENSG00000238009 RP11-34P13.7 ENSG00000239945 RP11-34P13.8 ENSG00000237683 AL627309.1 ENSG00000239906 RP11-34P13.14 ENSG00000241599 RP11-34P13.9 ENSG00000228463 AP006222.2 ENSG00000237094 RP4-669L17.10 (source: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices ) This is obviously the most useful option for well annotated organisms such as mouse and human (as it's easier to work with shorter, distinct gene names) but in my case, many of the gene names are the same and I was wondering if there was a way to read in gene_ids instead (i.e. the 1st column in the genes.tsv file from the CellRanger output), and if not, if this could be an option in 'Read10X'? Failing this, would anyone have any advice on how to possibly manipulate the genes.tsv file post CellRanger output to allow me to read in a modified genes.tsv file? Thank you for any help you can give in advance! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#630>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADjuVYakGpRt7nOwL_mNKCVaw2WCJLEFks5uIHLOgaJpZM4VWQfl> .

[andyrussell]

Brilliant, thank you very much!