Create a new SPE object without the 3 samples with poor histology about spatialdlpfc

[lcolladotor]

Thanks to LieberInstitute/spatialLIBD@848e207, you can now use the argument sample_order in the vis_grid*() functions. This means that don't need to read in the samples in any specific way, unlike what I had said earlier. You can see how I use it at LieberInstitute/Visium_SPG_AD@852798a

[lcolladotor]

We'll now use the output from /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/processed-data/rerun_spaceranger/ once it's all done. That will involve:

• Removing the Round.*/ portion from

  spatialDLPFC/code/analysis/01_build_SPE_final.R

  Lines 34 to 67 in 28a524f

  	sample_info <- data.frame(
  	sample_id = c(
  	"DLPFC_Br2743_ant_manual_alignment",
  	"DLPFC_Br2743_mid_manual_alignment_extra_reads",
  	"DLPFC_Br2743_post_manual_alignment",
  	"DLPFC_Br3942_ant_manual_alignment",
  	"DLPFC_Br3942_mid_manual_alignment",
  	"DLPFC_Br3942_post_manual_alignment",
  	"DLPFC_Br6423_ant_manual_alignment_extra_reads",
  	"DLPFC_Br6423_mid_manual_alignment",
  	"DLPFC_Br6423_post_extra_reads",
  	"DLPFC_Br8492_ant_manual_alignment",
  	"DLPFC_Br8492_mid_manual_alignment_extra_reads",
  	"DLPFC_Br8492_post_manual_alignment",
  	"Round4/DLPFC_Br2720_ant_2",
  	"Round2/DLPFC_Br2720_mid_manual_alignment",
  	"Round2/DLPFC_Br2720_post_extra_reads",
  	"Round4/DLPFC_Br6432_ant_2",
  	"Round2/DLPFC_Br6432_mid_manual_alignment",
  	"Round2/DLPFC_Br6432_post_manual_alignment",
  	"Round3/DLPFC_Br6471_ant_manual_alignment_all",
  	"Round3/DLPFC_Br6471_mid_manual_alignment_all",
  	"Round3/DLPFC_Br6471_post_manual_alignment_all",
  	"Round3/DLPFC_Br6522_ant_manual_alignment_all",
  	"Round3/DLPFC_Br6522_mid_manual_alignment_all",
  	"Round3/DLPFC_Br6522_post_manual_alignment_all",
  	"Round3/DLPFC_Br8325_ant_manual_alignment_all",
  	"Round4/DLPFC_Br8325_mid_2",
  	"Round3/DLPFC_Br8325_post_manual_alignment_all",
  	"Round3/DLPFC_Br8667_ant_extra_reads",
  	"Round3/DLPFC_Br8667_mid_manual_alignment_all",
  	"Round3/DLPFC_Br8667_post_manual_alignment_all"
  	),

• Changing NextSeq for rerun_spaceranger at

  spatialDLPFC/code/analysis/01_build_SPE_final.R

  Line 87 in 28a524f

  here::here("processed-data", "NextSeq"),

• Changing the GTF path from

  spatialDLPFC/code/analysis/01_build_SPE_final.R

  Line 105 in 28a524f

  reference_gtf = "/dcl02/lieber/ajaffe/SpatialTranscriptomics/refdata-gex-GRCh38-2020-A/genes/genes.gtf"

  to /dcs04/lieber/lcolladotor/annotationFiles_LIBD001/10x/refdata-gex-GRCh38-2020-A//genes/genes.gtf in order to match

  spatialDLPFC/code/spaceranger/rerun_spaceranger.sh

  Line 46 in 28a524f

  --transcriptome=/dcs04/lieber/lcolladotor/annotationFiles_LIBD001/10x/refdata-gex-GRCh38-2020-A \

  . They are identical, but just to use the more stable GTF file location.
• In order for

  spatialDLPFC/code/analysis/01_build_SPE_final.R

  Line 131 in 28a524f

  # file <- file.path(current, "spatial", "tissue_spot_counts.csv")

  to work, we need to finish #49, #48, and #40.

[lcolladotor]

Abby @abspangler13 let me know if you have questions about #41 (comment). Thanks!

[lcolladotor]

Now that #40 is done, @abspangler13 can you point me to new spe object once you have it? That way I can share it with BioTuring. Thanks!

EDIT: done with df53427