Shaun Jackman
Shaun Jackman
I haven't got to testing EMA just yet, and likely won't until after RECOMB. I'll let you know when I do though!
I'd like to recommend using `ema preproc` to decode barcodes for our linked read tools, [ABySS](https://github.com/bcgsc/abyss), [ARCS](https://github.com/bcgsc/arcs), and [Tigmint](https://github.com/bcgsc/tigmint). These tools expect `BX:Z` FASTQ files. Do you think you may...
That's excellent! Thanks, Ibrahim. I'll try it out and get back to you.
`ema preproc -b` works! Thanks, Ibrahim! One minor bug. When a read does not have a barcode assigned, the first read correctly outputs no barcode, but the second read outputs...
One more small request. I'd like to be able to specify the numeric suffix of the `BX:Z` tag when I have multiple Chromium libraries from the same sample (needed for...
The `-b` option of `ema preproc` is not yet in a released version. You'll need to compile the master branch from GitHub. With the [Homebrew](https://brew.sh) on macOS or [Linuxbrew](https://linuxbrew.sh) on...
The above `ema preproc -b` extracts the barcodes from the read sequence add puts it in the `BX:Z` tag of a FASTQ (not BAM) file. You can then use that...
`ema preproc -b` is faster alternative to `longranger basic`.
Hi, Ibarhim. I'm on vacation from mid-July to early August. We can discuss it further in August.
I'm trying this feature out now! First attempt ``` ema: src/techs.c:8: extract_bc_10x: Assertion `bc_str != NULL' failed. ``` `longranger basic` includes reads without barcodes, but they won't have a `BX:Z`...