custom transgenes

[JBreunig]

Brilliant package and super easy to use!

I am trying to add some custom transgenes (TagBFP2,EGFP, TdTomato, etc.) as I have successfully done in the past with CellRanger and StarSolo but I can't seem to get it to work. (They don't appear and the TE results differ with the custome ref.)

Specifically, I use: awk 'BEGIN{FS=OFS="\t"}{print $6,$7,$8,$11,$3,$10}' mus.rmsk.txt > mm10rmsk.bed

That comes out like this: chr1 3000000 3002128 L1_Mus3 105 - chr1 3003152 3003994 L1Md_F 268 - chr1 3003993 3004054 L1_Mus3 279 -

Then I run with tmp.gtf being the input I use for making my StarSolo, kbtools, or CellRanger refs with transgenes as additional chromosomes (I'm assuming this is the problem?): scTE_build -te mm10rmsk.bed -gene tmp.gtf -o custome

[Gtf tail] BFP2 BFP2 exon 1 89 . + 0 gene_id "BFP2"; transcript_id "BFP2.1"; gene_name "BFP2"; BFP2 BFP2 transcript 1 89 . + 0 gene_id "BFP2"; transcript_id "BFP2.1"; gene_name "BFP2"; mTom mTom exon 1 670 . + 0 gene_id "mTom"; transcript_id "mTom.1"; gene_name "mTom"; mTom mTom transcript 1 670 . + 0 gene_id "mTom"; transcript_id "mTom.1"; gene_name "mTom"; mGFP mGFP exon 1 207 . + 0 gene_id "mGFP"; transcript_id "mGFP.1"; gene_name "mGFP"; mGFP mGFP transcript 1 207 . + 0 gene_id "mGFP"; transcript_id "mGFP.1"; gene_name "mGFP";

And then: scTE -p 20 -i /star_out/PBS/Aligned.sortedByCoord.out.bam -o PBScustTE -x /custome.exclusive.idx --hdf5 True -CB CB -UMI UB

The custom transgenes are in the Bam.

But in Scanpy, the BFP2,mTom, and mGFP don't appear in the var_names with the genes and TEs. And the TEs are slightly different than I see when using your mm10 index.

Any suggestions?

Thanks in advance!

[JBreunig]

Happy to upload reference and sample if that's helpful.