Question: Where can I find the Space Ranger barcode whitelist and their coordinates on the slide?
Answer: Navigate to this directory in your Space Ranger installation:
(The exact path may vary based on the Space Ranger version you have installed).
The visium-v1_coordinates.txt file shows the coordinates of each barcode on the slide. 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 ==
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.