Delaney Sullivan

Yes, you would use this: `-1,0,0:0,0,3,1,0,3:0,3,0,1,3,0` Means you take the first 3-bp's of R1 and R2, and align your biological read from position 3 onward in R1 and R2.

Yeah, you can choose those options (see kb count which supports both). I haven't really seen a benefit for that though (with everything being 3' end, you can't really resolve...

Hi! Sorry for the semi-late reply (was traveling for the past week). 10XV1 requires three files: First file contains 14-bp barcode, second file contains the 10-bp UMI, and third file...

Can you show me the contents of your /sn_ovary/data/00_raw_data/input/raw_data/ folder? All the FASTQ files should be there.

Hmm, ok, so you only have an R1 and an R2 file (not three files). I'm not sure how to process data in this format because I have no ideas...

OK, based on the protocol provided, the technology appears to be 10xv3 (16 bp barcode, 12 bp UMIs -- R1 read length is 28 bp). So supply -x 10xv3 to...

Yes, you can just use —tcc for generating your TCC matrices — kb count does everything you need. Once you have generated your matrices, that’s when you start using Seurat...

This is a bit tricky. You're getting the TCCs which is NOT the same as isoforms. In any case, the first way would be the way to go if you...

You would need to use kallisto, not just kb-python. kallisto quant-tcc is what you would need to use. Unfortunately, I don't have a straightforward workflow for this written up but...

It should automatically parallelize (rather than sequential reading) if you enable many threads -- that's one reason that splitting FASTQ files into multiple chunks enables faster processing. kallisto should be...