How do I merge demultiplexed samples?

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Mosaic v3.4 can be used to merge two or more demultiplexed samples. Mosaic v3.4 can be installed following these instructions . After the successful installation, open your console/Anaconda prompt, activate the Mosaic environment, and check that the h5 merge command is available as well as its input parameters:

#To view the command line help
tapestri h5 merge samples -h

Usage: tapestri h5 merge samples [OPTIONS] [SRC]... DST

Merge samples from SRC into DST. SRC are two or more h5 files to merge. DST is the name of the file to create. If DST file already exists, it will be overwritten.

--chunked Obsolete. Merge samples is always done in chunks
--log DIRECTORY Path to logs folder
-h, --help Show this message and exit.

To merge the files run the command as:

tapestri h5 merge samples sample1.h5 sample2.h5....samplen.h5 merged_sample.h5

Where sample1-n.h5 are input and merged_sample.h5 is the output. This command will merge all the h5s listed in it and create a single merged h5 file as output.

Merging a DNA.h5 with a DNA+Protein.h5 will result in a DNA.h5, the protein data will be discarded. 

The merge function is not memory intensive and can typically be run on a laptop depending on the number of files to be merged. 

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