Why do I encounter this error when opening scTE?

[l1y1y]

$ scTE /public/home/zzs000213/.conda/envs/py3118/bin/scTE:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import('pkg_resources').run_script('scTE==1.0', 'scTE') DEBUG : Creating converter from 7 to 5 DEBUG : Creating converter from 5 to 7 DEBUG : Creating converter from 7 to 5 DEBUG : Creating converter from 5 to 7 usage: scTE [-h] [--min_genes INT] [--min_counts INT] [--expect-cells INT] [-f [input file format]] [-CB [{CR,CB,False}]] [-UMI [{UR,UB,False}]] [--keeptmp [{True,False}]] [--hdf5 [{True,False}]] [-p INT] [-v] -i INPUT [INPUT ...] -x ANNOGLB [ANNOGLB ...] -o [OUT] scTE: error: the following arguments are required: -i/--input, -x, -o/--out

[jphe]

I can't see any error, it's just waring messages

[OwenHoare1989]

Hello @jphe and @l1y1y

I was wondering if either of you could help me with my below question?

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

[l1y1y]

I can't see any error, it's just waring messages

It means can I continue to run this software? I am a beginner and don’t understand this very well.

[l1y1y]

Hello @jphe and @l1y1y

I was wondering if either of you could help me with my below question?

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

Sorry, I am also a beginner and don’t understand these very well.

[jphe]

@l1y1y Yes, you can continue

[l1y1y]

@l1y1y Yes, you can continue

Thank you, thank you very much for your reply