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:

  spatialDLPFC/code/spaceranger/spaceranger_parameters.txt

  Line 1 in 4c127da

  DLPFC_Br2743_ant_manual_alignment V19B23-075 A1 /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/Images/round1/Liebert_Institute_OTS-20-7690_rush_anterior_1.tif /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/images_raw_align_json/V19B23-075-A1_1_Br2743_ant_manual_alignment.json /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/FASTQ/2_DLPFC_Br3942_ant

• sample 4

  spatialDLPFC/code/spaceranger/spaceranger_parameters.txt

  Line 4 in 4c127da

  DLPFC_Br3942_ant_manual_alignment V19B23-075 B1 /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/Images/round1/Liebert_Institute_OTS-20-7690_rush_anterior_2.tif /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/images_raw_align_json/V19B23-075-B1_2_Br3942_ant_manual_alignment.json /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/FASTQ/3_DLPFC_Br6423_ant

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 269809d, 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:

• /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/processed-data/rerun_spaceranger/DLPFC_Br3942_ant_manual_alignment/outs/spatial/tissue_spot_counts.csv
• /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
• /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 269809d, those files didn't exist.

• DLPFC_Br3942_ant_manual_alignment corresponds to sample 4 (which we knew about already)

  spatialDLPFC/code/spaceranger/spaceranger_parameters.txt

  Line 4 in 4c127da

  DLPFC_Br3942_ant_manual_alignment V19B23-075 B1 /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/Images/round1/Liebert_Institute_OTS-20-7690_rush_anterior_2.tif /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/images_raw_align_json/V19B23-075-B1_2_Br3942_ant_manual_alignment.json /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/FASTQ/3_DLPFC_Br6423_ant

• DLPFC_Br6423_post_extra_reads corresponds to sample 9

  spatialDLPFC/code/spaceranger/spaceranger_parameters.txt

  Line 9 in 4c127da

  DLPFC_Br6423_post_extra_reads V19B23-073 C1 /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/Images/round1/Liebert_Institute_OTS-20-7748_rush_posterior_3.tif /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/images_raw_align_json/V19B23-073-C1_11_Br6423_post_manual_alignment.json /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/FASTQ/7_DLPFC_Br6423_mid,/dcs04/lieber/lcolladotor/rawDataTDSC_LIBD001/raw-data/2021-10-06_KMay110220/r1_sample10_L002_ds.6cea0b18c46c427db81aace3e84b8331,/dcs04/lieber/lcolladotor/rawDataTDSC_LIBD001/raw-data/2021-10-06_KMay110220/r1_sample10_L001_ds.21cbcc783c724f219328be5aa7f078f3

• DLPFC_Br2720_ant_2 corresponds to sample 28 (which we knew about already at Run VistoSeg for 2720 Ant (round 4) #40)

  spatialDLPFC/code/spaceranger/spaceranger_parameters.txt

  Line 28 in 4c127da

  DLPFC_Br2720_ant_2 V10B01-002 D1 /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/Images/round4/V10B01-002_D1_Br2720_ant_DLPFC.tif /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/images_raw_align_json/round4/V10B01-002-D1.json /dcs04/lieber/lcolladotor/rawDataTDSC_LIBD001/raw-data/2021-09-22_ASpa082421/4_L001_ds.7d02274e402d4635bc56094ffa6e0728,/dcs04/lieber/lcolladotor/rawDataTDSC_LIBD001/raw-data/2021-09-22_ASpa082421/4_L002_ds.52b7909924c143458260ea881e9bad52

• DLPFC_Br2720_post_extra_reads corresponds to sample 14

  spatialDLPFC/code/spaceranger/spaceranger_parameters.txt

  Line 14 in 4c127da

  DLPFC_Br2720_post_extra_reads V10U24-091 C1 /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/Images/round2/V10U24-091_C1_Br2720_DLPFC_post_3.tif /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/images_raw_align_json/round2/V10U24-091-C1_Br2770_post.json /dcs04/lieber/lcolladotor/rawDataTDSC_LIBD001/raw-data/2021-05-21_ASpa050421/3v_a_L002_ds.fa84fd9e56f341508825c991393cdca3,/dcs04/lieber/lcolladotor/rawDataTDSC_LIBD001/raw-data/2021-05-21_ASpa050421/3v_a_L001_ds.c7b5ef097ffa42ca99aa3c56ecc02654,/dcs04/lieber/lcolladotor/rawDataTDSC_LIBD001/raw-data/2021-09-22_ASpa050421/r2_sample3v_a_L002_ds.05ba070833ee454bab4244cd7b0fdd35,/dcs04/lieber/lcolladotor/rawDataTDSC_LIBD001/raw-data/2021-09-22_ASpa050421/r2_sample3v_a_L001_ds.8ed358ff823446d0815eb3af112cc4df

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 cf8430a, 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