Creating loom files

[abhisheksinghnl]

Hi,

My apologies in advance for a naive question. I am new to single cell RNA seq data analysis. I aim to create loom files for my scRNA data.

I have fastq that have been processed using STAR and I have three output files:

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

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

3. 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

My question is how can I generate a loom file from the above data.

I see that by using create::loom, can you please guide me through this function and also let me know, if I need anymore files then the ones that I have.

Thank you.

[mojaveazure]

I would use Matrix::readMM to read in the mtx file into R, add the row and column names from the tsv files, then use loomR::create to make your loom file.