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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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Making a new reference for 10X genomics data #62

Closed biobug16 closed 4 years ago

biobug16 commented 4 years ago

Hi @evolvedmicrobe and All, I want to build a new ref genome using cellranger to capture miRNA profile in scRNA data from 10X genomics. For which I started with UCSC gtf file and performed grep for "MIR" to get a filtered gtf file. This filtered gtf file was then used with mkref to build reference genome only for the miRNAs. But I am unable to use this genome further with cellranger count. Is that a correct approach? Correct me please if I am missing something.

Thanks

LehmannN commented 4 years ago

What's the error you get when you run cellranger count ? Your approach seems correct, just be careful if you took your GTF from the UCSC table browser, there are some known issues (check https://genome.ucsc.edu/FAQ/FAQdownloads.html#download37). If you got your data from there, I would recommend you to download the GTF file from here: https://hgdownload.soe.ucsc.edu/downloads.html

biobug16 commented 4 years ago

Hi @LehmannN , After downloding the GTF file again from the suggested link, it is working fine now. Thanks for your help.

LehmannN commented 4 years ago

I'm glad this helped ! You can close the issue now if you want.

biobug16 commented 4 years ago

Hi All and @LehmannN , I have a followup question, after mapping with filtered gtf using cellranger count with default settings, I found only 0.1% of mapping and 1 Median Genes per Cell. Do I need to change some parameters while mapping or I am doing anything incorrect. Any suggestions will be highly appreciated. Thanks