Changes between Version 19 and Version 20 of SOP/scRNA-seq


Ignore:
Timestamp:
08/25/20 14:32:39 (4 years ago)
Author:
ibarrasa
Comment:

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  • SOP/scRNA-seq

    v19 v20  
    1212bsub cellranger mkgtf Homo_sapiens.GRCh38.93.gtf Homo_sapiens.GRCh38.93.filtered.gtf --attribute=gene_biotype:protein_coding
    1313}}}
    14         * Create the cellranger index using a command such as 
     14        * Create the cellranger index using a command such as
    1515{{{
    1616bsub cellranger mkref --genome=MyGenome --fasta=genome.fa --genes=Genes.filtered.gtf --ref-version=1.0
    1717}}}
     18      * Optional: How to create a STAR index with parameters different than the defaults
     19        * Run the  "cellranger mkref" as specified above.
     20        * Look inside the "mkref" output folder for the "star" folder and the "genomeParameters.txt" file with the STAR command
     21        * Rerun the "STAR  --runMode genomeGenerate" command with the new parameters and use the output from this step to replace the original "star" folder inside the cellranger mkref output.
     22
    1823      * Run the actual [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count 'cellranger count'] command using syntax like
    1924{{{