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- l Input: FASTQ |
- l Output: BAM, MEX, CSV, HDF5, Web Summary, .cloupe/.loupe |
## Loupe Browser |
Loupe Browser is an interactive data visualization application that requires no prior programming knowledge. |
- l Input: .cloupe, .vloupe |
- l Output: Data visualization, including t-SNE and UMAP projections, custom clusters, differentially expressed genes |
- l Operating System: MacOS, Windows |
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## Troubleshooting |
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| GEM Generation & Barcoding | 67 | |
|------------------------------|------| |
71 |
## GEM Generation & Barcoding |
STEP |
1.2 |
Load Chromium GEM-X Chip |
## 1.4d |
After Chip is removed from the instrument and the wells are exposed. |
Normal |
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Gasket holes are aligned with the sample and gel bead wells. |
All recovery wells are similar in volume and opacity. |
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## Impacted |
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Gasket holes are misaligned with the gel bead wells. Open and close the chip holder slowly once. |
One of the rows of Chromium X/iX gasket will not align with the GEM-X chip. This is normal and will not impact the assay. |
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Recovery well A indicates a wetting failure. Not all wetting failures may present themselves with excess bubbles (foam). |
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Recovery wells A-C show normal emulsions. Not all normal emulsions may have small (in size and number) bubbles in the recovery wells. |
Inspecting emulsions in pipette tips is recommended for diagnosing emulsion failures. |
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## STEP |
1.4e Transfer GEMs |
from Chip All liquid levels are similar in volume and opacity without air trapped in the pipette tips. |
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## Normal |
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