mutli samples

[wangjiawen2013]

Dear,
Does velocyto support mutli samples ? I have nine 10x samples (nine .bam files) at different development stage, could I run them together with veloctyo ?

[pkharchenko]

You can try concatenating the resulting count spliced&unspliced count matrices. However, such design, in principle will have technical batch effects that can’t be controlled for.

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On Oct 15, 2018, at 9:41 AM, wangjiawen2013 ***@***.***> wrote: Dear, Does velocyto support mutli samples ? I have nine 10x samples (nine .bam files) at different development stage, could I run them together with veloctyo ? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#9>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALT78htBqGfT6wCNEjBekrNiVw0hKGP9ks5ulJBugaJpZM4XcXR3>.

[EularTang]

Merging multiple samples/lanes in a single file
The merging of different samples/lanes in the same loom file can be performed simply using the loompy library. This is usually just a single line:

loompy.combine(files, output_filename, key="Accession")
or if you want more control on the exact memory that is allocated or subset your data before merging you can do something like:

files = ["file1.loom","file2.loom","file3.loom","file4.loom"]

on the command line do: cp file1.loom merged.loom

ds = loompy.connect("merged.loom")
for fn in files[1:]:
ds.add_loom(fn, batch_size=1000)

[wangjiawen2013]

When combining data from multiple 10x genomics libraries, cellranger recommend equalizing the read depth between libraries before merging, to reduce the batch effect introduced by sequencing, the command is "cellranger aggr --nomalize=mapped". Will velocyto equalize the read depth per cell per sample when merging mutliple samples ?