Re-run VistoSeg on the 2 problematic samples

[lcolladotor]

Once SpaceRanger is done re-running for the 2 problematic samples, to be extra careful, we'll re-run VistoSeg to count the cells per spot in these 2 samples. They are:

• sample 1: https://github.com/LieberInstitute/spatialDLPFC/blob/4c127dafb03fa1b185168a22544453b55b833d97/code/spaceranger/spaceranger_parameters.txt#L1
• sample 4 https://github.com/LieberInstitute/spatialDLPFC/blob/4c127dafb03fa1b185168a22544453b55b833d97/code/spaceranger/spaceranger_parameters.txt#L4

Sample 1 already finished running on SpaceRanger and you can find the output at /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/processed-data/rerun_spaceranger/DLPFC_Br2743_ant_manual_alignment.

Sample 4 is queued at JHPCE. Once it's done, the output will be at /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/processed-data/rerun_spaceranger/DLPFC_Br3942_ant_manual_alignment.

Thanks @heenadivecha!

[lcolladotor]

@heenadivecha sample 4 is ready at /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/processed-data/rerun_spaceranger/DLPFC_Br3942_ant_manual_alignment

[lcolladotor]

From https://github.com/LieberInstitute/spatialDLPFC/commit/269809db4734f51503ca6f6e20cf10d13d7dd3aa, as it stands, we need the VistoSeg output for 4 samples:

DLPFC_Br3942_ant_manual_alignment
DLPFC_Br6423_post_extra_reads
DLPFC_Br2720_ant_2
DLPFC_Br2720_post_extra_reads

That is, we need to create or locate these files:

• [x] /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/processed-data/rerun_spaceranger/DLPFC_Br3942_ant_manual_alignment/outs/spatial/tissue_spot_counts.csv
• [x] /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/processed-data/rerun_spaceranger/DLPFC_Br6423_post_extra_reads/outs/spatial/tissue_spot_counts.csv
• [ ] /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/processed-data/rerun_spaceranger/DLPFC_Br2720_ant_2/outs/spatial/tissue_spot_counts.csv
• [x] /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/processed-data/rerun_spaceranger/DLPFC_Br2720_post_extra_reads/outs/spatial/tissue_spot_counts.csv

As far as I could tell at https://github.com/LieberInstitute/spatialDLPFC/commit/269809db4734f51503ca6f6e20cf10d13d7dd3aa, those files didn't exist.

• DLPFC_Br3942_ant_manual_alignment corresponds to sample 4 (which we knew about already) https://github.com/LieberInstitute/spatialDLPFC/blob/4c127dafb03fa1b185168a22544453b55b833d97/code/spaceranger/spaceranger_parameters.txt#L4
• DLPFC_Br6423_post_extra_reads corresponds to sample 9 https://github.com/LieberInstitute/spatialDLPFC/blob/4c127dafb03fa1b185168a22544453b55b833d97/code/spaceranger/spaceranger_parameters.txt#L9
• DLPFC_Br2720_ant_2 corresponds to sample 28 (which we knew about already at https://github.com/LieberInstitute/spatialDLPFC/issues/40) https://github.com/LieberInstitute/spatialDLPFC/blob/4c127dafb03fa1b185168a22544453b55b833d97/code/spaceranger/spaceranger_parameters.txt#L28
• DLPFC_Br2720_post_extra_reads corresponds to sample 14 https://github.com/LieberInstitute/spatialDLPFC/blob/4c127dafb03fa1b185168a22544453b55b833d97/code/spaceranger/spaceranger_parameters.txt#L14

These are some older files:

$ ls -lh */outs/spatial/tissue_spot_counts.csv
-rw-rw---- 1 lcollado lieber_lcolladotor 199K Jul 13 16:28 DLPFC_Br2720_ant_manual_alignment/outs/spatial/tissue_spot_counts.csv
-rw-rw---- 1 lcollado lieber_lcolladotor 198K Jul 19 12:15 DLPFC_Br6432_ant_manual_alignment/outs/spatial/tissue_spot_counts.csv
-rw-rw---- 1 lcollado lieber_lcolladotor 201K Aug  4 14:12 DLPFC_Br8325_mid_manual_alignment_all/outs/spatial/tissue_spot_counts.csv
-rw-rw---- 1 lcollado lieber_lcolladotor 198K Aug  4 11:50 DLPFC_Br8667_ant_manual_alignment_all/outs/spatial/tissue_spot_counts.csv
 $ pwd
/dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/processed-data/NextSeq_not_used

I don't think that we can use any of these, including DLPFC_Br2720_ant_manual_alignment/outs/spatial/tissue_spot_counts.csv since DLPFC_Br2720_ant_2 is a new image/dissection.

[lcolladotor]

Even though I closed this issue with https://github.com/LieberInstitute/spatialDLPFC/commit/cf8430a4f1bdaa5d262f3b9e3468870a9d6df6d3, we are still missing one which is what #40 is tracking.

$ ls -lh processed-data/rerun_spaceranger/DLPFC_Br3942_ant_manual_alignment/outs/spatial/tissue_spot_counts.csv
-rw-rw---- 1 lcollado lieber_lcolladotor 198K Dec 14 17:47 processed-data/rerun_spaceranger/DLPFC_Br3942_ant_manual_alignment/outs/spatial/tissue_spot_counts.csv
$ ls -lh processed-data/rerun_spaceranger/DLPFC_Br6423_post_extra_reads/outs/spatial/tissue_spot_counts.csv
-rw-rw---- 1 lcollado lieber_lcolladotor 199K Dec 14 19:28 processed-data/rerun_spaceranger/DLPFC_Br6423_post_extra_reads/outs/spatial/tissue_spot_counts.csv
$ ls -lh processed-data/rerun_spaceranger/DLPFC_Br2720_ant_2/outs/spatial/tissue_spot_counts.csv
ls: cannot access processed-data/rerun_spaceranger/DLPFC_Br2720_ant_2/outs/spatial/tissue_spot_counts.csv: No such file or directory
$ ls -lh processed-data/rerun_spaceranger/DLPFC_Br2720_post_extra_reads/outs/spatial/tissue_spot_counts.csv
-rw-rw---- 1 lcollado lieber_lcolladotor 199K Dec 14 17:37 processed-data/rerun_spaceranger/DLPFC_Br2720_post_extra_reads/outs/spatial/tissue_spot_counts.csv