different versions of CR mkfastq/(count-vdj)

10x_Workflows.md

@@ -264,7 +264,7 @@ There are two ways to solve this collision. One is to set the parameter `--barco
 
 ### Multiple `cellranger mkfastq` processes writing on the same directory  
 
-Occasionally, multiple `cellranger mkfastq` processes running on the same machine can attempt to write on the same directory. These processes can be spawned from the same call to `cellranger mkfastq`. When a `cellranger mkfastq` process attempts to write on a directory, it checks the file `<mkfastq_dir>/_lock`, where `<mkfastq_dir>` is the directory created by `cellranger mkfastq`. Ocassionally, if this file is created by other process, then the running process cannot write on the directory and returns an error. This is a concurrency error that, to the best of our knowledge, has not been solved by 10x. Since it is non-deterministic, the same command `cellranger mkfastq` can be executed with the same parameters until it finishes without errors. More information can be found [here](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/troubleshooting).
+Occasionally, A single call to `cellranger mkfastq` spawns multiple processes running on the same machine. This is done in order to speed up the generation of FASTQs files through multi-process parallelism. The results from each individual process need to be merged into a common directory of FASTQs files, so multiple processes can attempt to write on the same directory. When a `cellranger mkfastq` process attempts to write on a directory, it checks the file `<mkfastq_dir>/_lock`, where `<mkfastq_dir>` is the directory created by `cellranger mkfastq`. Ocassionally, if this file is created by other process, then the running process cannot write on the directory and returns an error. This is a concurrency error that, to the best of our knowledge, occurs on Cellranger version `3.1.0` and has not been solved by 10x. Since it is non-deterministic, the same command `cellranger mkfastq` can be executed with the same parameters until it finishes without errors. An alternative is to run `cellranger mkfastq` using version `3.0.2` (that does not have this error) and run `cellranger count` or `cellranger vdj` using either version `3.1.0` or `3.0.2`. A reason to use different versions of Cellranger for generating the FASTQs and counting the sequences is that, unlinke `cellranger count` version `3.0.2`, `cellranger count` version `3.1.0` counts sequences in sets of FASTQ files in which no Gene expression sequencing library is available. In order to do so, the current YAML configuration files permit using different versions of Cellranger for `cellranger mkfastq` and `cellranger count`. More information can be found [here](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/troubleshooting).
 
 ### 2. Libraries CSV
 |  FASTQs | Sample  |  Library Type |