Comparing celltypes from multiple samples.

[AidenSb]

Hi Vivian,
I'm trying to compare two celltypes. but reads are coming from multiple samples. do you suggest I extract the cells from each sample to a single bam file or multiple bam files?
to clarify I have ~1000 cells from 4 samples. I can extract celltypes A and B from these 4 Bam files and end up with 4 Cell A bam files and 4 Cell B bam files. then I can input these bam files to the bam_c1 and 2.
Alternatively, I can merge these bam files to one bam file and end up with one bam file per cell type. Which one is preferred for the MAPPER analysis or it doesn't matter?

[Vivianstats]

Hi Aiden,

I would suggest to prepare 4 bam files for celltype A and 4 bam files for celltype B, and input them as bam_c1 and bam_c2.
When you have 4 samples, this may not make a big difference; however, when you have more samples and paired test is desired, such input is required by MAAPER to produce the right results.

Best,
Vivian

[AidenSb]

Hi Vivian,
Thanks for the explanation, Indeed I have way more than 4 samples! one experiment has up to 20 samples ( control) and the other has like 10(treatment). So just to make sure if I understood correctly do you suggest to merge these to one big bam file? or proceed with multiple bams per condition?