list of real barcodes for Drop-seq technology

[ste-depo]

Hi everybody,

I'm trying to use your pipeline to analyze Drop-seq data with velocyto, but at the time of running dropEst we realized that the file with the list of real barcodes for the Drop-seq technology is not present in the expected folder (data/barcodes), while for other technology that file is there.

Also, trying to run dropEst and avoiding the usage of this file (no -m or -M options), do not seems to work because the software still looks for the barcode files. This mode of running dropEst is highly discouraged, therefore it would be better to have the barcode list file available.

Can anyone help?

All the best!
Stefano

[BoxWong]

Yep, a barcode file for drop-seq would be of great help!

Just something related: I've used drop-seq tools to do the preprocess followed by velocyto. I ran velocyto without specifying 10x or drop-seq whatsoever, and I did NOT give any barcode file either. Additionally, I modified the BAM tag of cell barcode from "XC" to "CB" in the header and the body of the bam file generated by drop-seq tools. Finally, it worked but the run took a pretty long time (possibly due to the absence of barcode files). Hope this helps!

But I agree that a barcode file for drop-seq would come in handy!