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

[EularTang]

Hi gioelelm， 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!

[gioelelm]

If you only need "any" loom file, surely you can change the format of your expression but if you need the special loom file that is used by velocity that contains spliced and unspliced read counted separately in two different matrices, no you can't. The information about their discrimination is not anymore present in the counting matrix.

To the second question: yes it is the best way, there might be other ways (e.g. one could merge the fastq files or bam files) but this would be the more direct one.

[ychniu]

If you only need "any" loom file, surely you can change the format of your expression but if you need the special loom file that is used by velocity that contains spliced and unspliced read counted separately in two different matrices, no you can't. The information about their discrimination is not anymore present in the counting matrix.

To the second question: yes it is the best way, there might be other ways (e.g. one could merge the fastq files or bam files) but this would be the more direct one.

Can I get the gene expression matrix from both spliced and unspliced reads and use these two matrices to get the loom file suitable for velocity analysis? Thanks!