Open andreyurch opened 2 weeks ago
Hi,
Thanks for your interest in COMPASS!
Thank you very much for your answers!
And the last question: if I preprocess my h5 files myself, how I have to normalise read count (CNV) table for genes? Should I take a sum or a mean of the amplicons? How does it work for whole chromosomes?
You can sum the read counts in each region (gene or chromosome) if you preprocess the data yourself.
You can sum the read counts in each region (gene or chromosome) if you preprocess the data yourself.
Thank you. I found that whitelist file for preprocessing contains a lot of information (which I do not have for my dataset). Is it possible to use the whitelist with only chr,pos,ref,alt?
Yes, most of the columns in the example mutations.csv are useless for the preprocessing script. You only need: sample ID, chr, start, ref allele, alt allele (the names of the columns are important). sample ID has to match the name of the loom file (e.g. if the loom file is sampleX.loom, then sample ID should be sampleX.
Dear developers,
Thank you very much for this advanced tool. I have a number of questions on modelling of CNVs on Tapestri data (thousands of cells and 400 amplicons):