Quang Nguyen

Hi Saket -- I think I am in similar situation. I think @greensii does want to integrate the control merged object (which he merged 5 different control replicates) with the...

Hi @longmanz - Thank you for your response. For Q1 and 2, did you mean that if we simply merge without merging `pca`, the algorithm would just put cells which...

Hi @ivirshup and @emdann -- My apologies for not understanding the recommended solutions here; would you mind explaining how we can solve this (save the AnnData object as h5da with...

@mihem -- Is the ref genome gtf file the one you downloaded (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz) or is it the one here instead (http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.primary_assembly.annotation.gtf.gz)? Issue #319 Thank you!

Hi @RBBurl1227 and @rekham1077 -- When you said you redo the alignment with new annotation file, did you mean you rerun the cellranger count or you meant you just use...

According to https://github.com/pysam-developers/pysam/issues/939: "This is a diagnostic that is new (in these circumstances) in HTSlib 1.10. In the context in which pysam is calling it it is just a warning...

No idea either lol. Please would you mind letting us know here if you find out something about this? Thanks @JerryZhang-1222

@Suger0917 -- My bam file does have CB and UB as you boxed in your comment back in Sep 25 2018 above, but it still gives me the error "the...

@Suger0917 did you have to modify the script provided by @snower2010 somehow for your own data, or you just use the same? And if you had to, how did you...

@saeedfc -- When you manually sort your bam first, did you then need to use the original bam.bai (index) file that came with the cellranger count? Or, did you have...