I am just running the scTE pipeline because I am very interested in studying transposable elements (TEs) in scRNA-seq data. Briefly, I used cellranger pipeline with a custome build human genome reference with TEs present in my GTF file. I use almost exactly the same STAR parameters with cellranger as was used in the scTE manuscript using the soloSTAR to allow for multi-mapping.
I used this BAM file from cellranger after allowing for multi-mapping and my generated custome hg38 index file to run the following command below.
The output seems to be only a csv file with genes and TEs. So my question is rather naive but how do I go from this output to a Seurat object. Cellranger outputs 3 files (genes, barcodes and matrix) which is needed to generate a Seurat object using the Seurat R package.
I mean am I supposed to use this 'out.csv' file from the scTE pipeline to merge to my Seurat object. I really don't understand. After alignment with TEs for bulk RNA-seq I can do feature counting and allow for multi-mapping. However, cellranger does not allow for this and this is why I was hoping this pipeline gives an interpretable output usable by Seurat. Am I missing something.
Could you please explain what I am supposed to use from this pipeline to obtain a Seurat object. I am very grateful for any help you can provide. If something is not clear please don't hesitate to ask.
Hi there,
I am just running the scTE pipeline because I am very interested in studying transposable elements (TEs) in scRNA-seq data. Briefly, I used cellranger pipeline with a custome build human genome reference with TEs present in my GTF file. I use almost exactly the same STAR parameters with cellranger as was used in the scTE manuscript using the soloSTAR to allow for multi-mapping.
I used this BAM file from cellranger after allowing for multi-mapping and my generated custome hg38 index file to run the following command below.
scTE -i inp.bam -o out -x mm10.exclusive.idx -CB False -UMI False
The output seems to be only a csv file with genes and TEs. So my question is rather naive but how do I go from this output to a Seurat object. Cellranger outputs 3 files (genes, barcodes and matrix) which is needed to generate a Seurat object using the Seurat R package.
I mean am I supposed to use this 'out.csv' file from the scTE pipeline to merge to my Seurat object. I really don't understand. After alignment with TEs for bulk RNA-seq I can do feature counting and allow for multi-mapping. However, cellranger does not allow for this and this is why I was hoping this pipeline gives an interpretable output usable by Seurat. Am I missing something.
Could you please explain what I am supposed to use from this pipeline to obtain a Seurat object. I am very grateful for any help you can provide. If something is not clear please don't hesitate to ask.
Thanks