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cellranger mkref

Hello,

I'm trying to build a reference for Macaca mulatta using this tutorial https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_mr#getfiles

I follow the same steps because I found it at the bottom of the page. When I arrived at this step

#Filter GTF
    cellranger mkgtf \
      Macaca_mulatta.Mmul_10.105.gtf Macaca_mulatta.Mmul_10.105.filtered.gtf \
      --attribute=gene_biotype:protein_coding \
      --attribute=gene_biotype:lincRNA \
      --attribute=gene_biotype:antisense \
      --attribute=gene_biotype:IG_LV_gene \
      --attribute=gene_biotype:IG_V_gene \
      --attribute=gene_biotype:IG_V_pseudogene \
      --attribute=gene_biotype:IG_D_gene \
      --attribute=gene_biotype:IG_J_gene \
      --attribute=gene_biotype:IG_J_pseudogene \
      --attribute=gene_biotype:IG_C_gene \
      --attribute=gene_biotype:IG_C_pseudogene \
      --attribute=gene_biotype:TR_V_gene \
      --attribute=gene_biotype:TR_V_pseudogene \
      --attribute=gene_biotype:TR_D_gene \
      --attribute=gene_biotype:TR_J_gene \
      --attribute=gene_biotype:TR_J_pseudogene \
      --attribute=gene_biotype:TR_C_gene

It says cellranger: command not found

I have already installed it What is the problem?

cellranger
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updated by Ram Ram • written by Zqall • Zqall

1 answer

cellranger: command not found

You need to append directory containing cellranger executable to your $PATH (see: https://www.cs.purdue.edu/homes/bb/cs348/www-S08/unix_path.html )

Otherwise use /full/path/to/cellranger in your command above.

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written by GenoMax GenoMax

THANK YOU!! It worked!

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written by Zqall • Zqall

Accept GenoMax's answer to mark the post as solved.

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written by Ram Ram

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