Delaney Sullivan

The whitelist I attached previously has ~900,000 entries with each barcode being 27 bp long -- is your whitelist.txt the same as or similar to the one I attached? In...

Great! Thanks, I think your whitelist only has 96x96x96 entries. The BD whitelist that I attached has 97x97x97 entries but everything in your whitelist is in the whitelist I attached...

Where are the sample tag sequences in your fastq files? Are they in the R1 file, the R2 file, or in some separate fastq file?

Do you know what position they are in the R2 file and how long the sequences are?

You could make the sample tags as part of the barcodes. The default scheme for `-x BDWTA` is `-x 0,0,9,0,21,30,0,43,52:0,52,60:1,0,0` which means taking 9+9+9 base pair barcodes from file #0...

The issue is 183055283:183055283 is an invalid coordinate (it has length 0). Such a coordinate should not exist in a properly formatted GTF file. It seems to me like it's...

The command looks correct. Running the nucleus index takes a lot of RAM, so your home computer may not have enough memory.

See https://github.com/pachterlab/kallisto/issues/303

We do have a filter to improve false discovery rate: https://rdrr.io/github/pachterlab/sleuth/man/sleuth_prep.html (see the filter options there, the default is the basic_filter)

Hello! 1) Correct, the EM algorithm is applied in kallisto quant. There's no way to avoid counting these multimapping reads in kallisto quant; doing would be a bad idea (it...