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huyustats / SCATS

A statistical tool to detect differential alternative splicing events using single-cell RNA-seq
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10X genomic scRNA-seq data #4

Open lahongxu opened 4 years ago

lahongxu commented 4 years ago

Hi, I am going to use SCATS to analyze 10x scRNA-seq data. After running cellranger, I can only get one bam file containing many cells. How can I generate metafile for SCATS step2? Can you give an example for it?

zhanglab2008 commented 3 years ago

I have the same question. Can the author provide more example codes to get the correct input files? The current tutorial is not detailed enough. I also have difficulty in generating the refgene file with the correct format. Hope the authors can spend a bit more time to polish the protocol. Many thanks!

ziyili20 commented 3 years ago

I generated metafile for 10x scRNA-seq data using R. What I did is to read in the barcode file for each sample (the files in /outs folder from cellranger output) and merge the barcode information with the condition and the other two columns as suggested by the tutorial. But the difficulty I met is, since our data has 80,000+ cells, the SCATS count step generated 80,000+ .sh files to run. I tried one .sh file today and found it took more than 5 hours to complete one job. Then having 80,000 jobs all completed seems to be an impossible task... I am not sure if I did this correctly.

zhanglab2008 commented 2 years ago

I generated metafile for 10x scRNA-seq data using R. What I did is to read in the barcode file for each sample (the files in /outs folder from cellranger output) and merge the barcode information with the condition and the other two columns as suggested by the tutorial. But the difficulty I met is, since our data has 80,000+ cells, the SCATS count step generated 80,000+ .sh files to run. I tried one .sh file today and found it took more than 5 hours to complete one job. Then having 80,000 jobs all completed seems to be an impossible task... I am not sure if I did this correctly.

@ziyili20 I tried your methods and it works on my side too. Thanks! But I have the same issue re: the running time...