Entering edit mode
5.8 years ago
Dataminer
★
2.8k
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.
