10xGenomics single cell multiome linked samples: 10x_multiome_libraries.info
For a run with 10xGenomics single cell multiome gene expression or
ATAC data, an additional file 10x_multiome_libraries.info
can
be created which indicates where the complementary ATAC or GEX
data are located.
If this file exists then it will be used by run_qc
to run the cellranger-arc
single library analysis for each sample
listed in the file (if it is absent then the single library analysis
is skipped).
The file should consist of one line for each sample in the project, with two fields separated by a tab:
<SAMPLE> [RUN][:PROJECT][/COMPLEMENTARY_SAMPLE]
For example:
AA_multiome_ATAC 201031_NB0123_000011_AHXXXX:AA/AA_multiome_GEX
Note
RUN
can be specified as a full path to an analysis
directory (e.g. /data/201031_NB0123_000011_AHXXXX_analysis
),
the name of an analysis directory (e.g.
201031_NB0123_000011_AHXXXX_analysis
), the name of a run
(e.g. 201031_NB0123_000011_AHXXXX
) or a run reference ID
(e.g. NEXTSEQ_201031#11
).
If a path is not supplied then the parent directory structure will be scanned to try and locate the specified analysis directory.
Note
Lines starting with a comment character (#
) will be
ignored when setting up the single library analysis.