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.