Hassan Massalha

Thanks for your help. Really I just wasted a lot of time trying to make this working! I will try also to save the seurat object and move to work...

Hi, Thanks for your help. I managed to solve the problem. I am getting another type of problem with the `RunVelocity `command. I getting the following message: ``` > seu

I have another suggestion for treating multiple samples. Do you think it is a good idea to attach artificial barcodes (2 letters) to the cell barcodes at the fastq files...

Hi, I don't have any NA in my data... ``` > which(is.na(as.matrix(seu@assays$spliced@counts))) integer(0) > which(is.na(as.matrix(seu@assays$spliced@data))) integer(0) > which(is.na(as.matrix(seu@[email protected]))) integer(0) > which(is.na(as.matrix(seu@assays$unspliced@counts))) integer(0) > which(is.na(as.matrix(seu@assays$unspliced@data))) integer(0) > which(is.na(as.matrix(seu@[email protected]))) ``` here is...

Hi, Thanks again for your help. I managed to run the pipeline to the end. My previous problem caused by low-quality cells. After applying more stringent preprocessing steps I managed...

Thanks for your input, I think in my case the separate isoforms are not optimal. I will test again with the collapsed setting. After updating the `BUSpaRse ` I am...

regarding the `-x` flag... I am using MARSseq chemistry which is: - R1: sequence read (length 66) - R2: plate_barcode (4pb)-cell_barcode(7bp)-UMI(8bp) my `-x` flag was as follows: `1,0,11:1,12,19:0,0,0` but I...

Dear @lambdamoses Any suggestion to solve the above issue? I think this is the source of other bugs that I have in the down stream analysis. Best HM

Thanks for your reply, I just tried your suggestion and used `1,0,12:1,12,19:0,0,0`and get the following output after running `bustools text` command: ``` GCTTGCTACTCC TAAGGCA 1547760 1 GCTTAGTCTCCG GGCGGTC 809667 1...

Great, thanks for your help. I am getting exactly the length that I am looking for. Now the next command in the pipeline (`bustools correct` and `bustools sort`) giving the...