Can I get a loom file from the gene expression matrix ?

[EularTang]

Dear, Can loom files be obtained only by the bam file after alignment? Can I get a loom file from the gene expression matrix which is easier to download?If there are 100 fastq data in an experiment, Is the only way that I align them in turn and then assemble these loom files into a total loom? For example，how did you achieve the loom file from GSE104323?（https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104323） Thank for your attention!

[Sophia409]

@EularTang Hello, I have the same confusion as you.And have you found the better solution?

[slinnarsson]

There are many ways to create a loom file (see loompy.org, especially the documentation), including from an expression matrix (e.g. from a 10x cellranger output).

However, in order to run velocyto, you need counts both for spliced and unspliced RNAs separately, which are normally not present in expression matrices. For that, you need to reanalyze the BAM files (or FASTQ files).

If you do happen to have expression matrices for both spliced and unspliced, separately, then of course you can easily create a loom file from that (using loompy.create(...)).