Question: Where can I find the Space Ranger barcode inclusion list and their coordinates on the slide?
Answer: Navigate to this directory in your Space Ranger installation:
spaceranger-x.y.z/lib/python/cellranger/barcodes
(The exact path may vary based on the Space Ranger version you have installed).
The *_coordinates.txt files show the coordinates of each barcode on the slide for the different chemistries. For slide serial numbers starting with V1, you will want the files labeled visium-v1. The other files are for slide serial numbers starting with the corresponding label, V2, V3, V4 and V5. For Visium v2 chemistry with CytAssist, which support FFPE tissues only, the slides will start with V4 and V5.
Here are the first five lines as an example:
head -n 5 visium-v1_coordinates.txt
AAACAACGAATAGTTC 17 1 AAACAAGTATCTCCCA 103 51 AAACAATCTACTAGCA 44 4 AAACACCAATAACTGC 20 60 AAACAGAGCGACTCCT 95 15
The three columns of this file are barcode, X coordinate, and Y coordinate. Note that the spots are arranged using "orange crate packing". This offsetting of spots increases the packing density. To represent this packing method not every possible x,y coordinate will have a spot associated with it.
Here is an example of orange crate packing:
This can be seen in the visium-v1_coordinates.txt file by sorting by the X coordinates followed by the Y coordinates. For the column with an X coordinate of 1, there are only odd values for Y:
sort -k2,2 -k3,3 -n visium-v1_coordinates.txt | head -n 5
ACGCCTGACACGCGCT 1 1
ACAGGAGGCGCAGCCG 1 3
CTAATGCGCCCAACAA 1 5
AGTGGGAGTATACACG 1 7
CTGTCTGTGGCTGGCT 1 9
For the column with the X coordinate of 2, there are only even values:
sort -k2,2 -k3,3 -n visium-v1_coordinates.txt | perl -lane 'print if $F[1] ==
2;' | head -n 5
TACCGATCCAACACTT 2 2 AGGCAATACGGAGGAC 2 4 GCCACCCATTCCACTT 2 6 GGTCTTGGTGTTAACT 2 8 ATATTATCCCGTATTT 2 10
This alternating pattern of odd and even Y coordinates generates the orange crate packing pattern.