Question: creating loom files using loomR
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gravatar for Dataminer
7 days ago by
Dataminer2.5k
Netherlands
Dataminer2.5k wrote:

Hi All,

Has anyone here created a loom file using loomR package in R.

The single cell RNA seq (10x) experiment files were processed using STAR and I have following files:

1. barcode.tsv
AAACCTGAGAACTCGG-1
AAACCTGAGTAGGCCA-1
AAACCTGGTCGAAAGC-1
AAACCTGTCCTTAATC-1
AAACCTGTCGCGTAGC-1
AAACCTGTCGTGACAT-1
AAACGGGAGTTAAGTG-1
AAACGGGCACAGGTTT-1
AAACGGGGTGCGCTTG-1
AAACGGGTCTGCGGCA-1

2. matrix.mtx
%%MatrixMarket matrix coordinate integer general
%
27998 3903 5884446
27921 1 13
27919 1 2
27918 1 8
27917 1 1
27916 1 1
27915 1 36
27914 1 49

3. Genes.tsv
ENSMUSG00000051951      Xkr4
ENSMUSG00000089699      Gm1992
ENSMUSG00000102343      Gm37381
ENSMUSG00000025900      Rp1
ENSMUSG00000109048      Rp1
ENSMUSG00000025902      Sox17
ENSMUSG00000104328      Gm37323
ENSMUSG00000033845      Mrpl15
ENSMUSG00000025903      Lypla1
ENSMUSG00000104217      Gm37988

the function is described here https://rdrr.io/github/mojaveazure/loomR/man/create.html#heading-4

but with no community example. Can anyone guide me through it.

Thank you.

rna-seq loomr • 55 views
ADD COMMENTlink modified 7 days ago • written 7 days ago by Dataminer2.5k
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