Question: I have sequenced the same 5' Gene Expression library twice with different sequencing configurations: 150x150 and 26x98. How to run Cell Ranger on all the raw data?
Answer: If you have data from multiple sequencing runs of the same library, you need to specify all FASTQ files in a single analysis of either cellranger count or cellranger multi.
In the case of a 5' Gene Expression library sequenced with 150x150 and 26x98 configuration (or other custom configurations), Cell Ranger cannot auto-detect if the library is SC5P-R2 (5' R2-only, where only R2 is used for alignment) or SC5P-PE (5' paired-end, where both R1 and R2 are used for alignment. R1 needs to be longer than 81 bases).
Therefore, in such cases, Cell Ranger needs to be run with chemistry as SC5P-R2.
If the chemistry is not specified, Cell Ranger will emit this error:
Log message:
We detected an unsupported chemistry combination (SC5P-R2, SC5P-PE). To process this combination of data you will need to specify SC5P-R2 via the --chemistry argument.
Related Articles:
- How does Cell Ranger auto-detect chemistry?
- Can I sequence my V(D)J libraries in a different sequencing configuration?
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