I am currently working on analyzing transposable element expression in human Placental cells. I would like to add a column to the Seurat object's metadata for what class of transposable element the barcode aligns to. I have a data frame of significant transposable elements detected by SoloTE, that have columns listing both the TE and the class ("SINE", "LINE", etc.). I would like to align this information in the Seurat metadata where I the same information, in which I would be able to plot the counts of TE as a whole. How am I able to get the feature name with a barcode, where then I could just make a method adding the feature name to the Seurat object and giving each gene a TE class. I'm not sure if STAR has changed, or SoloTE changes the features.tsv, but I saw a GitHub suggestion where both the barcode and gene name were stored together in features.tsv, but for some reason all SoloTE does is create a .tsv with the gene name taking up two columns, no barcode. I'm aware that Seurat does not have any updates regarding feature-specific metadata and of the sort, so if anyone knows what I could do please let me know!
Seurat Metadata:
orig.ident nCount_RNA nFeature_RNAsample percent_mt percent.mt predicted.annotation.l1.score predicted.annotation.l1 predicted.annotation.l2.score predicted.annotation.l2 predicted.organ.score predicted.organ mapping.score integrated_snn_res.0.3 seurat_clusters
AAACCCAGTACGTAGG_1 Control 15961 5813 Control 2.34947685 2.34947685 0.780277806 PAEP_MECOM positive cells 0.780277806 Placenta-PAEP_MECOM positive cells 0.871025485 Placenta 0.835290861 3 3
Significant TEs:
p_val avg_log2FC pct.1 pct.2 p_val_adj cluster gene class
SoloTE-chr2-102344418-102344708-L2c:L2:LINE-29.2-+ 0 2.586468475 0.408 0.071 0 PAEP_MECOM positive cells SoloTE-chr2-102344418-102344708-L2c:L2:LINE-29.2-+ LINE
SoloTE-chr12-12915018-12915204-AluJb:Alu:SINE-13.9-- 2.9472001078709e-253 3.121277459 0.277 0.04 3.96105168097903e-247 PAEP_MECOM positive cells SoloTE-chr12-12915018-12915204-AluJb:Alu:SINE-13.9-- SINE
SoloTE-chr8-24197937-24198396-LTR108b-Mam:ERVL:LTR-23.4-+ 8.8028074066327e-224 3.562187964 0.161 0.013 1.18310171685514e-217 PAEP_MECOM positive cells SoloTE-chr8-24197937-24198396-LTR108b-Mam:ERVL:LTR-23.4-+ LTR
SoloTE-chr9-114786633-114786941-AluYj4:Alu:SINE-7.4-+ 6.00397532422589e-215 2.505720999 0.276 0.046 8.06937285563621e-209 PAEP_MECOM positive cells SoloTE-chr9-114786633-114786941-AluYj4:Alu:SINE-7.4-+ SINE
SoloTE-chr4-188942887-188943065-MSTA:ERVL-MaLR:LTR-15.3-+ 2.07994014716876e-190 3.29115071 0.17 0.019 2.79544995749555e-184 PAEP_MECOM positive cells SoloTE-chr4-188942887-188943065-MSTA:ERVL-MaLR:LTR-15.3-+ LTR
SoloTE-chr4-188945069-188946618-L1PREC2:L1:LINE-13.8-+ 6.15065468348503e-183 3.742696156 0.142 0.013 8.2665106478773e-177 PAEP_MECOM positive cells SoloTE-chr4-188945069-188946618-L1PREC2:L1:LINE-13.8-+ LINE
SoloTE-chr1-155308054-155308366-AluSx3:Alu:SINE-7.0-- 3.72801958389383e-172 2.124631379 0.356 0.091 5.01047696085123e-166 PAEP_MECOM positive cells SoloTE-chr1-155308054-155308366-AluSx3:Alu:SINE-7.0-- SINE
SoloTE-chr19-41260299-41260611-AluSz:Alu:SINE-12.5-- 5.6464470409709e-168 2.135251388 0.302 0.068 7.5888530553001e-162 PAEP_MECOM positive cells SoloTE-chr19-41260299-41260611-AluSz:Alu:SINE-12.5-- SINE
SoloTE-chr8-24166049-24166234-L1PREC2:L1:LINE-14.5-+ 1.51913018061639e-167 3.308390742 0.135 0.013 2.04171855839933e-161 PAEP_MECOM positive cells SoloTE-chr8-24166049-24166234-L1PREC2:L1:LINE-14.5-+ LINE
SoloTE-chr8-117948077-117948131-L4-C-Mam:RTE-X:LINE-21.8-- 1.85972782880849e-164 1.910392079 0.384 0.107 2.49948350055775e-158 PAEP_MECOM positive cells SoloTE-chr8-117948077-117948131-L4-C-Mam:RTE-X:LINE-21.8-- LINE
